SLGI (version 1.32.0)

seqMatcherAlign: Functions to do local alignment of two sequences using EMBOSS matcher

Description

seqMatcherAlign matches two sequences using the EMBOSS matcher program.

getAlignStats extract the statistics from the alignment result data.

Usage

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

Arguments

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

Value

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

Details

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.

References

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

Examples

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)