seqMatcherAlign: Functions to do local alignment of two sequences using EMBOSS...
In SLGI: Synthetic Lethal Genetic Interaction

Description Usage Arguments Details Value Note Author(s) References Examples

seqMatcherAlign matches two sequences using the EMBOSS matcher program.

getAlignStats extract the statistics from the alignment result data.

1 2	seqMatcherAlign(pairNameV,BankIDV,seqBank) getAlignStats(alignRes)

`pairNameV`	a vector of gene pair names
`BankIDV`	a vector of the sequence IDs in the sequence Bank.
`seqBank`	a database of all the sequences
`alignRes`	object returned by `seqMatcherAlign`

seqMatcherAlign matches the gene pair names with the sequence bank IDs and export the two sequences in to two files: seq1.new and seq2.new. Then uses system calls to run EMBOSS matcher program to align the two sequences. The result from matcher is store in file "out.matcher". seqMatcherAlign read in this file and create a R object summarize the alignment results.

getAlignStats takes the alignment result data and extract the statistics of the result in to data.frame.

`names`	contains the names of the gene pair
`results`	contains the alignment statistics: the aligned total length, the number of identical match, the number of similar match, the number of gaps, and the alignment score
`seq`	displays the aligned sequences

pairMatcherAlign use system calls to run EMBOSS matcher program. You must have EMBOSS matcher installed on your computer.

Z. Jiang

EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276–277

seq1 <- "RPHEDEKEAIDEAKKMKVPGENEDESKEEEKSQELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENEHTAPPALVMPSPIEMEEQRM"
seq2 <- "QKYLLKKAIRNFSEYPFYAQNKLIHQQATGLILTEEEKSQELEEKIISKIKKEEHLKKINLKHDYFDLQKKYEKECEILTKLSENLRKEK"
seq3 <- "IHQQATGLILTKIISKIKKEEHVPGENEDLKKINLKHDYFDLQKKYEKECEILTKLSENLRKEEIENKRKEHELMEQKRREEGIETEKEKSLRHPSSSSSSRRRN"
seqBank <- list(seq1=list(seq=seq1),seq2=list(seq=seq2),seq3=list(seq=seq3))
bid <- names(seqBank)
pnames <- c("seq1","seq3")
## Not run: 
ar <- seqMatcherAlign(pnames, bid, seqBank)
ar
getAlignStats(ar)

## End(Not run)