Description Usage Arguments Details Value Author(s) Examples
Calculate alignments of one or more query sequences to a sequence database using the blat tool.
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query |
A character vector containing the sequence(s) to be aligned. The character vector is interprented fasta file where elements in the vector are lines. |
database |
A reference to the database to align with. |
eval |
Numerical threshold e-value. Only alignments with an e-value equal or smaller than |
tileSize |
tile size which blat will use See blat documentation for details |
add.parm |
Additional options to be passed to blat can be set here. |
The function executes "blat ....." and retrieves the results. Execute system("blat")
to get an overview of the options which can be passed to the add.parm
.
The function returns a data.frame containing the blat result for all submitted sequences; one row per alignment. The columns in the output contain the following information with respect to the alignment.
query |
Name of query sequence. |
sequence |
Name of sequence in the data base. |
mlength |
Length of the match. |
identity |
percent identy of the match. |
mismatches |
The number of mismatches in the alignment. |
gaps |
The number of gaps in the alignment. |
qstart |
The start of the match in the query. |
qstop |
The end of the match in the query. |
sstart |
The start of the match in the query. |
sstop |
The end of the match in the query. |
eval |
The e-value of the match. |
bitscore |
The the bit-score of the match. |
Wim de Leeuw (w.c.deLeeuw@uva.nl)
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