msaConservationScore-methods: Computation of Conservation Scores from Multiple Alignment
In msa: Multiple Sequence Alignment
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
This method computes a vector of conservation scores from a
multiple alignment or a previously computed consensus matrix.
Usage
1
2
3
4
5
## S4 method for signature 'matrix'
msaConservationScore(x, substitutionMatrix, gapVsGap=NULL,
...)
## S4 method for signature 'MultipleAlignment'
msaConservationScore(x, ...)
Arguments
x
an object of class MultipleAlignment
(which includes objects of classes
MsaAAMultipleAlignment,
MsaDNAMultipleAlignment, and
MsaRNAMultipleAlignment) or a previously
computed consensus matrix (see details below).
substitutionMatrix
substitution matrix (see
details below).
gapVsGap
score to use for aligning gaps versus gaps (see
details below).
...
when the method is called for a
MultipleAlignment object, the consensus matrix is
computed and, including all further arguments,
passed on to the msaConservationScore method with signature
matrix. This method passes all further arguments on to the
msaConsensusSequence method to customize the way
the consensus sequence is computed.
Details
The method takes a MultipleAlignment object or a
previously computed consensus matrix and computes the sum of pairwise
scores for all positions of the alignment. For computing these scores,
it is compulsory to specify a substitution/scoring matrix. This matrix
must be provided as a matrix object. This can either be
one of the ready-made matrices provided by the Biostrings
package (e.g. BLOSUM62) or any other hand-crafted
matrix. In the latter case, the following restrictions apply:
The matrix must be quadratic.
For reasonable results, the matrix should be symmetric (note
that this is not checked).
Rows and columns must be named and the order of letters/symbols
in row names and column names must be identical.
All letters/symbols occurring in the multiple alignment,
including gaps ‘-’, must also be found in the row/column
names of the substitution matrix. For consistency with the
matrices from the Biostrings package, the
row/column corresponding to gap penalties
may also be labeled ‘*’ instead of ‘-’.
So, nucleotide substitution matrices created by
nucleotideSubstitutionMatrix can be used for multiple
alignments of nucleotide sequences, but must be
completed with gap penalty rows and columns (see example below).
If the consensus matrix of a multiple alignment of nucleotide
sequences contains rows labeled ‘+’ and/or ‘.’, these
rows are ignored.
The parameter gapVsGap can be used to control how
pairs of gaps are scored. If gapVsGap=NULL (default), the
corresponding diagonal entry of the substitution matrix is used as is.
In the BLOSUM matrices, this is usually a positive value, which may
not make sense under all circumstances. Therefore, the parameter
gapVsGap can be set to an alternative value, e.g. 0 for
ignoring gap-gap pairs.
The method, in any case, returns a vector of scores that is as long
as the alignment/consensus matrix has columns. The names of the vector
entries are the corresponding positions of the consensus sequence of
the alignment. How this consensus sequence is computed, can be
controlled with additional arguments that are passed on to the
msaConsensusSequence method.
Value
The function returns a vector as long as the alignment/consensus
matrix has columns. The vector is named with the consensus sequence
(see details above).
Author(s)
Ulrich Bodenhofer <msa@bioinf.jku.at>
References
http://www.bioinf.jku.at/software/msa
U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
(2015). msa: an R package for multiple sequence alignment.
Bioinformatics 31(24):3997-3999. DOI:
10.1093/bioinformatics/btv494.
See Also
msa, MsaAAMultipleAlignment,
MsaDNAMultipleAlignment,
MsaRNAMultipleAlignment,
MsaMetaData,
MultipleAlignment,
msaConsensusSequence
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
## read sequences
filepath <- system.file("examples", "HemoglobinAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)
## perform multiple alignment
myAlignment <- msa(mySeqs)
## compute consensus scores using the BLOSUM62 matrix
data(BLOSUM62)
msaConservationScore(myAlignment, BLOSUM62)
## compute consensus scores using the BLOSUM62 matrix
## without scoring gap-gap pairs and using a different consensus sequence
msaConservationScore(myAlignment, BLOSUM62, gapVsGap=0,
type="upperlower")
## compute a consensus matrix first
conMat <- consensusMatrix(myAlignment)
data(PAM250)
msaConservationScore(conMat, PAM250, gapVsGap=0)
## DNA example
filepath <- system.file("examples", "exampleDNA.fasta", package="msa")
mySeqs <- readDNAStringSet(filepath)
## perform multiple alignment
myAlignment <- msa(mySeqs)
## create substitution matrix with gap penalty -8
mat <- nucleotideSubstitutionMatrix(4, -1)
mat <- cbind(rbind(mat, "-"=-8), "-"=-8)
## compute consensus scores using this matrix
msaConservationScore(myAlignment, mat, gapVsGap=0)
Example output
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
use default substitution matrix
- V L S ? A D K ? N V K A ? W G
5 681 1156 913 210 314 1605 1445 327 968 1052 1163 479 179 2854 376
K ? G G H A ? E Y G A E A L E R
1104 824 928 422 1625 606 353 745 1764 1181 637 1445 920 1156 547 1445
M F ? S F P T T K T Y F P H F -
793 1540 11 434 976 2023 680 1445 1445 1445 2023 1734 1143 2022 1389 132
D L S H G S A Q V K G H G K K V
1605 760 842 722 1480 1156 625 965 960 1220 533 2053 1734 1028 1253 1096
A D A L T ? A V ? H ? D D L P G
555 955 1156 976 506 126 1156 595 251 1625 610 1605 1434 744 745 514
A L S A L S D L H A H K L R V D
792 1093 1060 446 1156 1156 1605 1156 2312 1156 1352 1109 1156 1349 1156 1734
P V N F K L L S H C L L V T L A
2023 626 1734 1734 1135 724 1156 637 1715 1298 778 873 1156 909 888 1060
? H ? P A ? F T P A V H A S L D
89 1956 90 1479 352 703 1366 1074 2023 481 792 1956 735 976 921 1734
K F L A ? V S T V L T S K Y R
1445 1734 838 370 291 952 796 929 1028 1156 1165 937 1349 2023 1445
- v L s a a d K t n v k a a w g
-220 681 1156 913 210 314 1605 1445 327 968 1052 1163 479 179 2854 376
k v g g h a g e y g a E a L e R
1104 824 928 422 1625 606 353 745 1764 1181 637 1445 920 1156 547 1445
m f l s f P t T K T Y F p h f -
793 1540 11 434 976 2023 680 1445 1445 1445 2023 1734 1143 2022 1389 -124
d l s h g S a q v k g h G k k v
1605 760 842 722 1480 1156 625 965 960 1220 533 2053 1734 1028 1253 1096
a d A l t . A v a h l d d l p g
555 955 1156 976 506 126 1156 595 251 1625 610 1605 1434 744 745 514
a l s a L S d L H A h k L r V D
792 1093 1060 446 1156 1156 1605 1156 2312 1156 1352 1109 1156 1349 1156 1734
P v N F k l L s h c l l V t l a
2023 626 1734 1734 1135 724 1156 637 1715 1298 778 873 1156 909 888 1060
. h h p a d f t P a v h a s l D
89 1956 90 1479 352 703 1366 1074 2023 481 792 1956 735 976 921 1734
K F l a s v s t v L t s k Y R
1445 1734 838 370 291 952 796 929 1028 1156 1165 937 1349 2023 1445
- V L S ? A D K ? N V K A ? W G
-456 760 1734 503 361 322 1124 1445 314 376 1172 1222 359 11 4361 522
K ? G G H A ? E Y G A E A L E R
1105 999 878 508 1305 493 530 649 2533 1019 468 1156 522 1734 519 1734
M F ? S F P T T K T Y F P H F -
1011 2374 -52 277 1514 1734 467 867 1445 867 2890 2601 1150 1572 2067 -254
D L S H G S A Q V K G H G K K V
1124 1266 498 756 1222 578 385 940 1119 1190 524 1636 1445 1026 1283 1160
A D A L T ? A V ? H ? D D L P G
306 801 578 1486 410 100 578 549 335 1305 922 1124 1028 1146 806 533
A L S A L S D L H A H K L R V D
402 1670 546 262 1734 578 1124 1734 1734 578 999 1165 1734 1637 1156 1156
P V N F K L L S H C L L V T L A
1734 715 578 2601 1135 1261 1734 412 1386 1710 1181 1325 1156 571 1290 546
? H ? P A ? F T P A V H A S L D
-70 1478 138 1370 299 728 2169 684 1734 348 848 1478 317 518 1430 1156
K F L A ? V S T V L T S K Y R
1445 2601 1425 244 162 1045 471 535 1026 1734 741 486 1382 2890 1734
use default substitution matrix
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - ? G T C C ? G G ? C ? G G ? G - ? ?
-28 -28 -26 -16 -16 -16 -16 -26 -16 -16 -26 -16 -26 -16 -16 -26 -16 -28 -26 -26
? G G ? ? ? ? ? ? C ? G ? ? ? ? ? ? ? C
-26 -16 -16 -26 -26 -26 -26 -26 -26 -16 -26 -16 -26 -26 -26 -26 -26 -26 -26 -16
? ? T ? ? ? C T ? C T ? C G T C A G G ?
-26 -26 -16 -26 -26 -26 -16 -16 -26 -16 -16 -26 -16 -16 -16 -16 -16 -16 -16 -26
C A A ? ? C C - C ? ? ? G ? G ? G T ? A
-16 -16 -16 -26 -26 -16 -16 -28 -16 -26 -26 -26 -16 -26 -16 -26 -16 -16 -26 -16
C ? ? T G ? ? G A ? - T G C A - - - - G
-16 -26 -26 -16 -16 -26 -26 -16 -16 -26 -28 -16 -16 -16 -16 -28 -28 -28 -28 -16
? ? ? G A G A C A C C C T T ? ? ? A A C
-26 -26 -26 -16 -16 -16 -16 -16 -16 -16 -16 -16 -16 -16 -26 -26 -26 -16 -16 -16
- T C T C ? T C T C C T - - C C ? ? A G
-28 -16 -16 -16 -16 -26 -16 -16 -16 -16 -16 -16 -28 -28 -16 -16 -26 -26 -16 -16
? G C C A G G T T A A A A C C A T C A G
-26 -16 -16 16 36 16 36 36 36 36 36 36 36 36 36 16 36 36 36 36
C C C - C ? C A T C C T G A G T G C A A
36 36 36 -28 36 6 36 16 36 16 36 36 36 16 16 36 36 36 16 16
A C C T T T C C ? A A C C C - - - - C G
36 36 16 36 16 16 36 16 6 16 36 36 36 16 -28 -28 -28 -28 16 16
C T G C T A A G C T A G A C A C C T C A
36 36 16 16 16 36 36 36 36 16 36 36 36 16 36 36 36 36 36 36
C T C A C T G A G A G C C A G C A T G G
36 36 16 16 36 16 36 16 36 36 36 36 36 36 36 36 36 36 36 16
C A G C T G T T G T C C T G G A G A A C
36 16 16 36 36 36 16 16 36 36 36 36 36 36 36 36 16 36 36 16
G G A G T C C T G A G C A G A A A A C T
16 16 36 36 16 36 16 36 36 16 36 36 36 36 16 36 36 36 36 36
C T C A G A C T T T G G G C A G G A A A
36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 36 36 36 36 36
C A A G C T A T A T T G A A G A C A A C
36 36 36 36 16 36 36 16 36 36 16 36 36 36 36 36 36 36 36 36
T C C A A T C A A A A T G G T G C C A T
36 16 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 16 36
A T C T C T G A T A T T C T C A C T C A
36 36 36 16 36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36
A A G A G G A A G T T G G T G C C C T G
36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 16 16 36 16
G C C A A G G T C C T G C G C T T A T T
36 36 36 36 36 16 36 36 16 16 36 36 36 36 36 36 36 36 36 36
T G A G G A G A A T G A T A T C A A C C
36 36 36 36 36 36 36 36 36 16 36 36 16 16 36 16 36 36 36 36
T G A C A C A C A T T G A A T C C A G A
36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36
C C T T C T C G T T T A A A C A A A G A
36 36 36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 36 36 36
T G A G T A T G A G T T T T T C A C C T
36 36 36 36 36 36 36 36 36 16 36 36 16 36 36 36 36 36 16 16
A T C T G G A T A A G C G T A G C A A G
36 36 16 36 36 36 36 36 36 36 16 36 36 36 36 36 36 16 16 16
C C T G T T C T G G G C A G C A T C A T
36 36 16 36 16 16 36 36 36 16 16 16 36 16 36 36 36 36 36 36
C A A G A G C C T G A G G A A T G A C A
36 36 36 36 36 16 36 16 36 36 36 36 36 16 36 16 36 36 36 36
T T G G T G C C A C T G T C C A T G A G
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36
C T T T C C C G A G A C A A G G A A A A
36 36 36 36 36 16 36 36 36 36 36 16 36 36 36 16 36 16 36 36
G A A C A C A G T G C C C T G G T T C C
16 16 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
C A A G G A C C A T T C A G G A G C T G
36 36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 36 16 36 36
G A C A G A T T C G C C A A T C A G A T
36 36 36 16 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36
T C T C A G C T A T G G A G C C G A A C
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36
T G G A T G C ? G A C C A C C C A G G C
36 36 36 36 36 36 36 6 36 36 36 36 36 36 36 36 16 36 36 16
T T T A A A G A T C C T G T G T A C C G
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
G G C G A G A C G A A A G C A G T T T G
16 36 36 16 36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36
C T G A C A T T G C C T A C A A C T A C
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
C G C C A T G G G C A G C C C A T C C C
36 36 36 36 36 36 36 36 16 36 36 36 36 36 36 36 36 16 36 36
T C G G G T G G A A T A C A C A G A G G
36 36 36 16 36 36 36 36 36 36 36 36 36 36 16 16 36 36 36 36
A A G A G A A G A A G A C C T G G G G A
36 16 36 36 16 36 16 36 16 36 16 36 36 16 36 36 36 36 36 16
A C G G T G T T C A G G A C T C T G A A
36 36 16 36 36 36 36 36 36 36 16 36 36 36 16 16 36 36 36 36
G G C C T T G T A T A A A A C A C A T G
36 16 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36
C C T G C T A C G A G C A C A A C C A C
36 16 36 36 36 36 36 16 36 36 36 16 36 36 36 36 16 36 36 36
A T T T T C C C A C T T C T G G A A A A
36 36 16 36 36 16 36 36 16 36 36 36 36 36 16 36 36 36 36 36
G T A C T G C G G T T T C C G T G A A G
36 36 36 36 36 36 16 36 36 16 36 36 36 36 16 36 36 36 36 36
A C A A C A T T C C ? C A G C T G G A A
36 16 36 36 36 36 36 16 36 36 6 36 36 36 36 36 36 36 36 36
G A T G T T T C T C A A T T T C T G C A
36 36 16 36 36 36 36 36 36 36 36 16 36 36 16 36 36 36 36 36
G A C T T G T A C T G G T T T C C G C C
36 36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 36 36
T C C G A C C T G T T G C T G G C T T A
36 36 36 36 16 36 36 36 36 36 16 36 36 36 36 36 36 16 36 16
C T G T C ? T C T C G A G A T T T C T T
36 36 16 36 36 6 36 36 36 36 36 16 36 36 36 36 36 36 36 36
G G G T G G C C T G G C C T T C C G A G
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
T C T T C C A C T G C A C A C A G T A C
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
A T T A G G C A T G G A T C ? A A G C C
36 36 16 36 36 16 36 36 36 36 36 36 36 36 6 36 36 36 36 36
C A T G T A C A C A C C T G A A C C T G
36 36 36 36 36 36 16 36 36 16 36 36 16 36 36 36 36 36 36 36
A C A T C T G C C A T G A A C T C T T G
36 16 36 36 36 36 36 16 36 36 36 36 36 16 36 36 16 36 36 36
G G A C A T G T G C C C T T G T T T T C
36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36 36 36 36 36
A G A T C G C A G C T T T G C C C A G T
36 36 36 36 16 36 16 36 36 36 36 36 36 36 36 36 36 36 36 36
T T T C T C A G G A A A T T G G G C T T
36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36
G C A T C ? C T G G G G G C A C C T G A
36 36 16 36 36 6 36 36 36 36 36 16 36 36 36 36 36 36 36 36
T G A G T A C A T T G A G A A A C T G G
36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 16 36 36 16 36
C C A C A A T T T A C T G G T T T A C T
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
G T G G A G T T T G G G C T T T G C A A
36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36 36
G G A A G G A G A T T C T A T A A A G G
16 16 36 36 36 36 36 36 36 16 36 36 16 36 36 36 36 36 36 36
C A T A T G G T G C T G G G C T C T T G
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36
T C A T C C T T T G G A G A A T T A C A
36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36 36 36 36 36
G T A C T G T T T A T C A G A C A A G C
36 36 36 36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 36 36
C A A A G C T C C T C C C C C T G G A G
36 36 36 36 36 36 36 16 36 36 16 36 36 36 36 36 36 36 36 36
C T A G A G A A G A C A G C C T G C C A
36 36 16 36 36 36 36 36 36 36 16 36 36 36 36 16 16 36 36 36
G G A G T A T A C T G T C A C A G A G T
16 16 36 16 36 36 16 16 36 36 36 36 36 36 36 16 36 36 36 36
T C C A G C C C C T G T A C T A C G T G
36 36 36 36 36 36 36 16 16 36 36 36 36 16 36 36 16 36 36 36
G C ? G A G A G T T T C A A T G A T G C
36 36 6 36 36 36 36 36 36 36 36 16 36 16 36 36 36 36 36 36
C A A G G A G A A A G T G A G G A C T T
36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36 16 16 36
T T G C T G C C A C A A T C C C T C G G
36 36 36 36 36 36 36 36 36 36 16 36 36 16 36 36 16 36 36 36
C C C T T C T C ? G T T C G C T A T G A
36 36 36 36 36 36 36 36 6 36 36 36 36 36 36 36 36 16 36 36
C C C ? T A C A C T C A A A G G G T T G
36 36 36 6 36 36 36 36 36 16 36 36 36 36 36 36 16 36 36 36
A G G T C C T G G A C A A T A C T C A G
36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 16 36 36 36
C A G T T G A A G A T T T T A G C T G A
36 36 36 16 36 16 36 36 36 36 36 36 36 36 16 36 36 36 36 36
C T C C A T T A A T A G T G A G G T T G
16 36 36 36 36 36 36 36 36 16 36 36 36 36 36 16 16 36 16 36
G A A T C C T T T G C A A T G C C C T G
36 36 36 36 36 36 36 36 36 36 36 16 16 36 36 36 36 36 36 16
C A G A A A A T A A A G T C ? T G A ? C
36 36 36 36 36 16 36 36 36 36 36 36 36 -16 -26 -16 -16 -16 -26 -16
A G A A A ? T G A C G T C A T G G A C A
-16 -16 -16 -16 -16 -26 -16 16 36 16 36 16 36 36 36 16 36 16 36 36
G A A C T T A G G A G G T C A A C C A ?
36 36 36 16 16 36 16 36 16 16 16 36 36 36 36 16 36 16 16 6
A A A - - T C T G T T G A T A G A A G T
16 36 36 -28 -28 36 36 16 36 16 16 36 36 36 16 36 36 16 16 36
A T A G T A A C T G C T T T T ? T T ? C
16 16 36 16 16 16 36 16 36 16 36 16 36 16 16 -26 36 16 6 16
C C T G A - - - - - A G A A G A A A A G
16 16 16 16 36 -28 -28 -28 -28 -28 36 16 36 36 16 16 36 36 36 16
T T T T A T T T G A A A T G T C A G C T
16 36 36 16 36 36 36 36 36 16 36 36 16 16 16 36 36 36 36 16
T T T A A T A T - T T T T C C T A A C A
36 36 16 36 16 36 -16 -16 -28 -16 -16 -16 16 16 16 36 16 36 36 36
? A G T G G A G ? A T C A C C A A A T A
6 16 16 36 36 36 36 36 6 36 16 36 36 16 36 36 36 36 36 36
A A T C A A A ? T T C T C T G A A A T G
36 16 36 36 36 36 16 -26 36 16 16 36 36 36 36 36 36 36 36 36
A A A G T A T A T T A A A A C C C A C C
36 16 36 36 16 16 36 16 36 16 36 16 16 36 36 16 16 16 16 16
- - - - - - - - - A G T G G T A G A T C
-28 -28 -28 -28 -28 -28 -28 -28 -28 36 16 16 36 36 36 36 16 36 36 36
T T T C A G A G T C A C A T T T G A T T
16 36 36 16 16 36 16 16 36 36 36 16 16 36 36 36 36 36 36 36
T A G A - - - - - T A A T C T C A T A C
36 36 36 36 -28 -28 -28 -28 -28 36 36 -16 36 36 16 36 36 16 36 16
C T T C A A T T T G G T T T A A A A T G
16 16 36 36 36 36 36 36 16 16 36 36 36 16 36 36 16 16 16 36
T A A T T T - C T C A G ? T C T C A T C
36 36 36 36 16 36 -28 16 36 36 16 16 6 36 16 36 36 36 36 36
A A C A T T C A T C A A A - T T T G G G
36 36 16 36 36 36 16 36 36 16 36 36 36 -28 36 36 36 36 36 36
A C T T G T ? T C A T T ? G G G C T T C
16 36 16 16 16 16 6 36 36 36 36 36 6 16 16 36 36 36 16 16
A T C T G T T C A T T T T T A A C C T C
16 36 16 16 16 36 -16 -16 -16 -16 -16 -16 -16 -16 -16 16 36 16 36 16
T C A G G T A A G C T C T G A A G G A A
16 36 36 36 16 16 36 36 16 16 16 16 36 16 36 16 36 36 36 16
C A C A T A T G G C T ? A G T G T A A A
16 36 16 36 36 16 16 16 36 36 36 6 36 16 36 36 36 36 36 36
A T G T A A G A C T G T C A T C A G G A
36 16 16 16 16 36 36 36 36 36 36 16 36 36 36 16 16 36 16 16
A T G A A T T A T T C C G T T C A G T A
16 16 16 36 36 36 16 36 36 36 16 16 16 16 36 16 36 16 36 36
C A G A T T G T A A T C T A C A A A G ?
16 36 16 36 36 16 36 36 36 36 16 36 36 36 16 16 36 36 36 6
T T A G T T T C T A C ? T T C G T T C A
16 36 36 16 36 36 36 16 16 36 16 6 36 36 16 16 36 36 16 36
T T A T G G C T C T G A G A A C T A C T
16 36 36 36 36 16 16 36 36 16 16 36 16 16 36 36 36 16 36 36
T T G T T A G C C T G C T T A C A T A A
36 36 36 36 36 36 16 16 16 36 16 36 16 36 36 16 16 36 36 36
A T ? T C C T C T G A T C ? A A G A C C
36 36 6 36 16 36 16 16 36 16 16 16 16 6 16 16 16 36 16 16
C T A T T A A G A T A G T T A C A A G C
36 16 36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 36
A A T A A A G T T ? T ? ? A G C A T T A
36 16 36 16 36 36 16 -16 -16 -26 -16 -26 -26 -16 -16 16 36 36 36 36
T A T A A A A A A A A A A A A A A A ? ?
36 36 36 16 36 36 16 16 16 36 36 36 36 36 16 36 16 16 -26 -26
? ? ? A ? ? ? ? ? ? - - - - - - - - - -
-26 -26 -26 -16 -26 -26 -26 -26 -26 -26 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
msa documentation built on Nov. 8, 2020, 5:41 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) References See Also Examples
Description
This method computes a vector of conservation scores from a multiple alignment or a previously computed consensus matrix.
Usage
1 2 3 4 5 | ## S4 method for signature 'matrix'
msaConservationScore(x, substitutionMatrix, gapVsGap=NULL,
...)
## S4 method for signature 'MultipleAlignment'
msaConservationScore(x, ...)
|
Arguments
x |
an object of class |
substitutionMatrix |
substitution matrix (see details below). |
gapVsGap |
score to use for aligning gaps versus gaps (see details below). |
... |
when the method is called for a
|
Details
The method takes a MultipleAlignment object or a
previously computed consensus matrix and computes the sum of pairwise
scores for all positions of the alignment. For computing these scores,
it is compulsory to specify a substitution/scoring matrix. This matrix
must be provided as a matrix object. This can either be
one of the ready-made matrices provided by the Biostrings
package (e.g. BLOSUM62) or any other hand-crafted
matrix. In the latter case, the following restrictions apply:
The matrix must be quadratic.
For reasonable results, the matrix should be symmetric (note that this is not checked).
Rows and columns must be named and the order of letters/symbols in row names and column names must be identical.
All letters/symbols occurring in the multiple alignment, including gaps ‘-’, must also be found in the row/column names of the substitution matrix. For consistency with the matrices from the Biostrings package, the row/column corresponding to gap penalties may also be labeled ‘*’ instead of ‘-’.
So, nucleotide substitution matrices created by
nucleotideSubstitutionMatrix can be used for multiple
alignments of nucleotide sequences, but must be
completed with gap penalty rows and columns (see example below).
If the consensus matrix of a multiple alignment of nucleotide sequences contains rows labeled ‘+’ and/or ‘.’, these rows are ignored.
The parameter gapVsGap can be used to control how
pairs of gaps are scored. If gapVsGap=NULL (default), the
corresponding diagonal entry of the substitution matrix is used as is.
In the BLOSUM matrices, this is usually a positive value, which may
not make sense under all circumstances. Therefore, the parameter
gapVsGap can be set to an alternative value, e.g. 0 for
ignoring gap-gap pairs.
The method, in any case, returns a vector of scores that is as long
as the alignment/consensus matrix has columns. The names of the vector
entries are the corresponding positions of the consensus sequence of
the alignment. How this consensus sequence is computed, can be
controlled with additional arguments that are passed on to the
msaConsensusSequence method.
Value
The function returns a vector as long as the alignment/consensus matrix has columns. The vector is named with the consensus sequence (see details above).
Author(s)
Ulrich Bodenhofer <msa@bioinf.jku.at>
References
http://www.bioinf.jku.at/software/msa
U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.
See Also
msa, MsaAAMultipleAlignment,
MsaDNAMultipleAlignment,
MsaRNAMultipleAlignment,
MsaMetaData,
MultipleAlignment,
msaConsensusSequence
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ## read sequences
filepath <- system.file("examples", "HemoglobinAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)
## perform multiple alignment
myAlignment <- msa(mySeqs)
## compute consensus scores using the BLOSUM62 matrix
data(BLOSUM62)
msaConservationScore(myAlignment, BLOSUM62)
## compute consensus scores using the BLOSUM62 matrix
## without scoring gap-gap pairs and using a different consensus sequence
msaConservationScore(myAlignment, BLOSUM62, gapVsGap=0,
type="upperlower")
## compute a consensus matrix first
conMat <- consensusMatrix(myAlignment)
data(PAM250)
msaConservationScore(conMat, PAM250, gapVsGap=0)
## DNA example
filepath <- system.file("examples", "exampleDNA.fasta", package="msa")
mySeqs <- readDNAStringSet(filepath)
## perform multiple alignment
myAlignment <- msa(mySeqs)
## create substitution matrix with gap penalty -8
mat <- nucleotideSubstitutionMatrix(4, -1)
mat <- cbind(rbind(mat, "-"=-8), "-"=-8)
## compute consensus scores using this matrix
msaConservationScore(myAlignment, mat, gapVsGap=0)
|
Example output
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
use default substitution matrix
- V L S ? A D K ? N V K A ? W G
5 681 1156 913 210 314 1605 1445 327 968 1052 1163 479 179 2854 376
K ? G G H A ? E Y G A E A L E R
1104 824 928 422 1625 606 353 745 1764 1181 637 1445 920 1156 547 1445
M F ? S F P T T K T Y F P H F -
793 1540 11 434 976 2023 680 1445 1445 1445 2023 1734 1143 2022 1389 132
D L S H G S A Q V K G H G K K V
1605 760 842 722 1480 1156 625 965 960 1220 533 2053 1734 1028 1253 1096
A D A L T ? A V ? H ? D D L P G
555 955 1156 976 506 126 1156 595 251 1625 610 1605 1434 744 745 514
A L S A L S D L H A H K L R V D
792 1093 1060 446 1156 1156 1605 1156 2312 1156 1352 1109 1156 1349 1156 1734
P V N F K L L S H C L L V T L A
2023 626 1734 1734 1135 724 1156 637 1715 1298 778 873 1156 909 888 1060
? H ? P A ? F T P A V H A S L D
89 1956 90 1479 352 703 1366 1074 2023 481 792 1956 735 976 921 1734
K F L A ? V S T V L T S K Y R
1445 1734 838 370 291 952 796 929 1028 1156 1165 937 1349 2023 1445
- v L s a a d K t n v k a a w g
-220 681 1156 913 210 314 1605 1445 327 968 1052 1163 479 179 2854 376
k v g g h a g e y g a E a L e R
1104 824 928 422 1625 606 353 745 1764 1181 637 1445 920 1156 547 1445
m f l s f P t T K T Y F p h f -
793 1540 11 434 976 2023 680 1445 1445 1445 2023 1734 1143 2022 1389 -124
d l s h g S a q v k g h G k k v
1605 760 842 722 1480 1156 625 965 960 1220 533 2053 1734 1028 1253 1096
a d A l t . A v a h l d d l p g
555 955 1156 976 506 126 1156 595 251 1625 610 1605 1434 744 745 514
a l s a L S d L H A h k L r V D
792 1093 1060 446 1156 1156 1605 1156 2312 1156 1352 1109 1156 1349 1156 1734
P v N F k l L s h c l l V t l a
2023 626 1734 1734 1135 724 1156 637 1715 1298 778 873 1156 909 888 1060
. h h p a d f t P a v h a s l D
89 1956 90 1479 352 703 1366 1074 2023 481 792 1956 735 976 921 1734
K F l a s v s t v L t s k Y R
1445 1734 838 370 291 952 796 929 1028 1156 1165 937 1349 2023 1445
- V L S ? A D K ? N V K A ? W G
-456 760 1734 503 361 322 1124 1445 314 376 1172 1222 359 11 4361 522
K ? G G H A ? E Y G A E A L E R
1105 999 878 508 1305 493 530 649 2533 1019 468 1156 522 1734 519 1734
M F ? S F P T T K T Y F P H F -
1011 2374 -52 277 1514 1734 467 867 1445 867 2890 2601 1150 1572 2067 -254
D L S H G S A Q V K G H G K K V
1124 1266 498 756 1222 578 385 940 1119 1190 524 1636 1445 1026 1283 1160
A D A L T ? A V ? H ? D D L P G
306 801 578 1486 410 100 578 549 335 1305 922 1124 1028 1146 806 533
A L S A L S D L H A H K L R V D
402 1670 546 262 1734 578 1124 1734 1734 578 999 1165 1734 1637 1156 1156
P V N F K L L S H C L L V T L A
1734 715 578 2601 1135 1261 1734 412 1386 1710 1181 1325 1156 571 1290 546
? H ? P A ? F T P A V H A S L D
-70 1478 138 1370 299 728 2169 684 1734 348 848 1478 317 518 1430 1156
K F L A ? V S T V L T S K Y R
1445 2601 1425 244 162 1045 471 535 1026 1734 741 486 1382 2890 1734
use default substitution matrix
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - ? G T C C ? G G ? C ? G G ? G - ? ?
-28 -28 -26 -16 -16 -16 -16 -26 -16 -16 -26 -16 -26 -16 -16 -26 -16 -28 -26 -26
? G G ? ? ? ? ? ? C ? G ? ? ? ? ? ? ? C
-26 -16 -16 -26 -26 -26 -26 -26 -26 -16 -26 -16 -26 -26 -26 -26 -26 -26 -26 -16
? ? T ? ? ? C T ? C T ? C G T C A G G ?
-26 -26 -16 -26 -26 -26 -16 -16 -26 -16 -16 -26 -16 -16 -16 -16 -16 -16 -16 -26
C A A ? ? C C - C ? ? ? G ? G ? G T ? A
-16 -16 -16 -26 -26 -16 -16 -28 -16 -26 -26 -26 -16 -26 -16 -26 -16 -16 -26 -16
C ? ? T G ? ? G A ? - T G C A - - - - G
-16 -26 -26 -16 -16 -26 -26 -16 -16 -26 -28 -16 -16 -16 -16 -28 -28 -28 -28 -16
? ? ? G A G A C A C C C T T ? ? ? A A C
-26 -26 -26 -16 -16 -16 -16 -16 -16 -16 -16 -16 -16 -16 -26 -26 -26 -16 -16 -16
- T C T C ? T C T C C T - - C C ? ? A G
-28 -16 -16 -16 -16 -26 -16 -16 -16 -16 -16 -16 -28 -28 -16 -16 -26 -26 -16 -16
? G C C A G G T T A A A A C C A T C A G
-26 -16 -16 16 36 16 36 36 36 36 36 36 36 36 36 16 36 36 36 36
C C C - C ? C A T C C T G A G T G C A A
36 36 36 -28 36 6 36 16 36 16 36 36 36 16 16 36 36 36 16 16
A C C T T T C C ? A A C C C - - - - C G
36 36 16 36 16 16 36 16 6 16 36 36 36 16 -28 -28 -28 -28 16 16
C T G C T A A G C T A G A C A C C T C A
36 36 16 16 16 36 36 36 36 16 36 36 36 16 36 36 36 36 36 36
C T C A C T G A G A G C C A G C A T G G
36 36 16 16 36 16 36 16 36 36 36 36 36 36 36 36 36 36 36 16
C A G C T G T T G T C C T G G A G A A C
36 16 16 36 36 36 16 16 36 36 36 36 36 36 36 36 16 36 36 16
G G A G T C C T G A G C A G A A A A C T
16 16 36 36 16 36 16 36 36 16 36 36 36 36 16 36 36 36 36 36
C T C A G A C T T T G G G C A G G A A A
36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 36 36 36 36 36
C A A G C T A T A T T G A A G A C A A C
36 36 36 36 16 36 36 16 36 36 16 36 36 36 36 36 36 36 36 36
T C C A A T C A A A A T G G T G C C A T
36 16 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 16 36
A T C T C T G A T A T T C T C A C T C A
36 36 36 16 36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36
A A G A G G A A G T T G G T G C C C T G
36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 16 16 36 16
G C C A A G G T C C T G C G C T T A T T
36 36 36 36 36 16 36 36 16 16 36 36 36 36 36 36 36 36 36 36
T G A G G A G A A T G A T A T C A A C C
36 36 36 36 36 36 36 36 36 16 36 36 16 16 36 16 36 36 36 36
T G A C A C A C A T T G A A T C C A G A
36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36
C C T T C T C G T T T A A A C A A A G A
36 36 36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 36 36 36
T G A G T A T G A G T T T T T C A C C T
36 36 36 36 36 36 36 36 36 16 36 36 16 36 36 36 36 36 16 16
A T C T G G A T A A G C G T A G C A A G
36 36 16 36 36 36 36 36 36 36 16 36 36 36 36 36 36 16 16 16
C C T G T T C T G G G C A G C A T C A T
36 36 16 36 16 16 36 36 36 16 16 16 36 16 36 36 36 36 36 36
C A A G A G C C T G A G G A A T G A C A
36 36 36 36 36 16 36 16 36 36 36 36 36 16 36 16 36 36 36 36
T T G G T G C C A C T G T C C A T G A G
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36
C T T T C C C G A G A C A A G G A A A A
36 36 36 36 36 16 36 36 36 36 36 16 36 36 36 16 36 16 36 36
G A A C A C A G T G C C C T G G T T C C
16 16 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
C A A G G A C C A T T C A G G A G C T G
36 36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 36 16 36 36
G A C A G A T T C G C C A A T C A G A T
36 36 36 16 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36
T C T C A G C T A T G G A G C C G A A C
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36
T G G A T G C ? G A C C A C C C A G G C
36 36 36 36 36 36 36 6 36 36 36 36 36 36 36 36 16 36 36 16
T T T A A A G A T C C T G T G T A C C G
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
G G C G A G A C G A A A G C A G T T T G
16 36 36 16 36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36
C T G A C A T T G C C T A C A A C T A C
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
C G C C A T G G G C A G C C C A T C C C
36 36 36 36 36 36 36 36 16 36 36 36 36 36 36 36 36 16 36 36
T C G G G T G G A A T A C A C A G A G G
36 36 36 16 36 36 36 36 36 36 36 36 36 36 16 16 36 36 36 36
A A G A G A A G A A G A C C T G G G G A
36 16 36 36 16 36 16 36 16 36 16 36 36 16 36 36 36 36 36 16
A C G G T G T T C A G G A C T C T G A A
36 36 16 36 36 36 36 36 36 36 16 36 36 36 16 16 36 36 36 36
G G C C T T G T A T A A A A C A C A T G
36 16 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36
C C T G C T A C G A G C A C A A C C A C
36 16 36 36 36 36 36 16 36 36 36 16 36 36 36 36 16 36 36 36
A T T T T C C C A C T T C T G G A A A A
36 36 16 36 36 16 36 36 16 36 36 36 36 36 16 36 36 36 36 36
G T A C T G C G G T T T C C G T G A A G
36 36 36 36 36 36 16 36 36 16 36 36 36 36 16 36 36 36 36 36
A C A A C A T T C C ? C A G C T G G A A
36 16 36 36 36 36 36 16 36 36 6 36 36 36 36 36 36 36 36 36
G A T G T T T C T C A A T T T C T G C A
36 36 16 36 36 36 36 36 36 36 36 16 36 36 16 36 36 36 36 36
G A C T T G T A C T G G T T T C C G C C
36 36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 36 36
T C C G A C C T G T T G C T G G C T T A
36 36 36 36 16 36 36 36 36 36 16 36 36 36 36 36 36 16 36 16
C T G T C ? T C T C G A G A T T T C T T
36 36 16 36 36 6 36 36 36 36 36 16 36 36 36 36 36 36 36 36
G G G T G G C C T G G C C T T C C G A G
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
T C T T C C A C T G C A C A C A G T A C
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
A T T A G G C A T G G A T C ? A A G C C
36 36 16 36 36 16 36 36 36 36 36 36 36 36 6 36 36 36 36 36
C A T G T A C A C A C C T G A A C C T G
36 36 36 36 36 36 16 36 36 16 36 36 16 36 36 36 36 36 36 36
A C A T C T G C C A T G A A C T C T T G
36 16 36 36 36 36 36 16 36 36 36 36 36 16 36 36 16 36 36 36
G G A C A T G T G C C C T T G T T T T C
36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36 36 36 36 36
A G A T C G C A G C T T T G C C C A G T
36 36 36 36 16 36 16 36 36 36 36 36 36 36 36 36 36 36 36 36
T T T C T C A G G A A A T T G G G C T T
36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36
G C A T C ? C T G G G G G C A C C T G A
36 36 16 36 36 6 36 36 36 36 36 16 36 36 36 36 36 36 36 36
T G A G T A C A T T G A G A A A C T G G
36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 16 36 36 16 36
C C A C A A T T T A C T G G T T T A C T
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36
G T G G A G T T T G G G C T T T G C A A
36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36 36
G G A A G G A G A T T C T A T A A A G G
16 16 36 36 36 36 36 36 36 16 36 36 16 36 36 36 36 36 36 36
C A T A T G G T G C T G G G C T C T T G
36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 16 36 36
T C A T C C T T T G G A G A A T T A C A
36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36 36 36 36 36
G T A C T G T T T A T C A G A C A A G C
36 36 36 36 36 36 16 36 36 36 36 36 36 36 36 16 36 36 36 36
C A A A G C T C C T C C C C C T G G A G
36 36 36 36 36 36 36 16 36 36 16 36 36 36 36 36 36 36 36 36
C T A G A G A A G A C A G C C T G C C A
36 36 16 36 36 36 36 36 36 36 16 36 36 36 36 16 16 36 36 36
G G A G T A T A C T G T C A C A G A G T
16 16 36 16 36 36 16 16 36 36 36 36 36 36 36 16 36 36 36 36
T C C A G C C C C T G T A C T A C G T G
36 36 36 36 36 36 36 16 16 36 36 36 36 16 36 36 16 36 36 36
G C ? G A G A G T T T C A A T G A T G C
36 36 6 36 36 36 36 36 36 36 36 16 36 16 36 36 36 36 36 36
C A A G G A G A A A G T G A G G A C T T
36 36 36 36 36 36 36 36 36 36 36 36 16 36 36 36 36 16 16 36
T T G C T G C C A C A A T C C C T C G G
36 36 36 36 36 36 36 36 36 36 16 36 36 16 36 36 16 36 36 36
C C C T T C T C ? G T T C G C T A T G A
36 36 36 36 36 36 36 36 6 36 36 36 36 36 36 36 36 16 36 36
C C C ? T A C A C T C A A A G G G T T G
36 36 36 6 36 36 36 36 36 16 36 36 36 36 36 36 16 36 36 36
A G G T C C T G G A C A A T A C T C A G
36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 16 36 36 36
C A G T T G A A G A T T T T A G C T G A
36 36 36 16 36 16 36 36 36 36 36 36 36 36 16 36 36 36 36 36
C T C C A T T A A T A G T G A G G T T G
16 36 36 36 36 36 36 36 36 16 36 36 36 36 36 16 16 36 16 36
G A A T C C T T T G C A A T G C C C T G
36 36 36 36 36 36 36 36 36 36 36 16 16 36 36 36 36 36 36 16
C A G A A A A T A A A G T C ? T G A ? C
36 36 36 36 36 16 36 36 36 36 36 36 36 -16 -26 -16 -16 -16 -26 -16
A G A A A ? T G A C G T C A T G G A C A
-16 -16 -16 -16 -16 -26 -16 16 36 16 36 16 36 36 36 16 36 16 36 36
G A A C T T A G G A G G T C A A C C A ?
36 36 36 16 16 36 16 36 16 16 16 36 36 36 36 16 36 16 16 6
A A A - - T C T G T T G A T A G A A G T
16 36 36 -28 -28 36 36 16 36 16 16 36 36 36 16 36 36 16 16 36
A T A G T A A C T G C T T T T ? T T ? C
16 16 36 16 16 16 36 16 36 16 36 16 36 16 16 -26 36 16 6 16
C C T G A - - - - - A G A A G A A A A G
16 16 16 16 36 -28 -28 -28 -28 -28 36 16 36 36 16 16 36 36 36 16
T T T T A T T T G A A A T G T C A G C T
16 36 36 16 36 36 36 36 36 16 36 36 16 16 16 36 36 36 36 16
T T T A A T A T - T T T T C C T A A C A
36 36 16 36 16 36 -16 -16 -28 -16 -16 -16 16 16 16 36 16 36 36 36
? A G T G G A G ? A T C A C C A A A T A
6 16 16 36 36 36 36 36 6 36 16 36 36 16 36 36 36 36 36 36
A A T C A A A ? T T C T C T G A A A T G
36 16 36 36 36 36 16 -26 36 16 16 36 36 36 36 36 36 36 36 36
A A A G T A T A T T A A A A C C C A C C
36 16 36 36 16 16 36 16 36 16 36 16 16 36 36 16 16 16 16 16
- - - - - - - - - A G T G G T A G A T C
-28 -28 -28 -28 -28 -28 -28 -28 -28 36 16 16 36 36 36 36 16 36 36 36
T T T C A G A G T C A C A T T T G A T T
16 36 36 16 16 36 16 16 36 36 36 16 16 36 36 36 36 36 36 36
T A G A - - - - - T A A T C T C A T A C
36 36 36 36 -28 -28 -28 -28 -28 36 36 -16 36 36 16 36 36 16 36 16
C T T C A A T T T G G T T T A A A A T G
16 16 36 36 36 36 36 36 16 16 36 36 36 16 36 36 16 16 16 36
T A A T T T - C T C A G ? T C T C A T C
36 36 36 36 16 36 -28 16 36 36 16 16 6 36 16 36 36 36 36 36
A A C A T T C A T C A A A - T T T G G G
36 36 16 36 36 36 16 36 36 16 36 36 36 -28 36 36 36 36 36 36
A C T T G T ? T C A T T ? G G G C T T C
16 36 16 16 16 16 6 36 36 36 36 36 6 16 16 36 36 36 16 16
A T C T G T T C A T T T T T A A C C T C
16 36 16 16 16 36 -16 -16 -16 -16 -16 -16 -16 -16 -16 16 36 16 36 16
T C A G G T A A G C T C T G A A G G A A
16 36 36 36 16 16 36 36 16 16 16 16 36 16 36 16 36 36 36 16
C A C A T A T G G C T ? A G T G T A A A
16 36 16 36 36 16 16 16 36 36 36 6 36 16 36 36 36 36 36 36
A T G T A A G A C T G T C A T C A G G A
36 16 16 16 16 36 36 36 36 36 36 16 36 36 36 16 16 36 16 16
A T G A A T T A T T C C G T T C A G T A
16 16 16 36 36 36 16 36 36 36 16 16 16 16 36 16 36 16 36 36
C A G A T T G T A A T C T A C A A A G ?
16 36 16 36 36 16 36 36 36 36 16 36 36 36 16 16 36 36 36 6
T T A G T T T C T A C ? T T C G T T C A
16 36 36 16 36 36 36 16 16 36 16 6 36 36 16 16 36 36 16 36
T T A T G G C T C T G A G A A C T A C T
16 36 36 36 36 16 16 36 36 16 16 36 16 16 36 36 36 16 36 36
T T G T T A G C C T G C T T A C A T A A
36 36 36 36 36 36 16 16 16 36 16 36 16 36 36 16 16 36 36 36
A T ? T C C T C T G A T C ? A A G A C C
36 36 6 36 16 36 16 16 36 16 16 16 16 6 16 16 16 36 16 16
C T A T T A A G A T A G T T A C A A G C
36 16 36 36 36 36 36 16 36 36 36 36 36 36 36 36 36 36 36 36
A A T A A A G T T ? T ? ? A G C A T T A
36 16 36 16 36 36 16 -16 -16 -26 -16 -26 -26 -16 -16 16 36 36 36 36
T A T A A A A A A A A A A A A A A A ? ?
36 36 36 16 36 36 16 16 16 36 36 36 36 36 16 36 16 16 -26 -26
? ? ? A ? ? ? ? ? ? - - - - - - - - - -
-26 -26 -26 -16 -26 -26 -26 -26 -26 -26 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
- - - - - - - - - - - - - - - -
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.