[BioC] difference results by needle program and pairwiseAlignment

[Lapointe, David]

I am not sure what your issue is. These sequences do not align well at all anyway. Global alignment is probably not a good way to compare them. There are large gaps at each end and 72% of the alignment ( according to needle) are gaps. Does pairwiseAlignment penalize end gaps? What score did pairwiseAlignment report?

David

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Wang Peter
Sent: Thursday, December 06, 2012 4:15 PM
To: bioconductor at r-project.org
Subject: [BioC] difference results by needle program and pairwiseAlignment

i used EMBOSS package needle program got the score 6

pairwiseAlignment(seq1,seq2, type = "global", substitutionMatrix = "BLOSUM62", gapOpening = -10, gapExtension = -0.5)

both use the same parameter

# Matrix: EBLOSUM62
# Gap_penalty: -10.0
# Extend_penalty: -0.5
		
sequences are
>AAG19119.1
mgitkqvsirsdnfipghrvfderpHILHvcdikvnpednmwefeyqkekdeissrhtkdvylymeldekqhskltsffl
eekprdssHSFHvdisgdiiqqvtkrpgagtsdkeknkytpspirfealsdrvvietfagdnpiipyyevthhdtpqdrh
nvsriesfiqsmqdggstpgleplptelvselqsaewgeevrHHLHegdecyrnsllhpalssyihaiewalisflkeke
dvdiiqqekngdlyyfasgnsilgevqdtgelsqksisrikslnraerrwmghhksgeatkeeldgmrarltqileelfg
tdsark
>AAG19157.1
msvaddstddHGHHlpavedwpkgfgeaswwpfitaigaagfyigaalyvlgrgesalvgpmvgpgvfiastfaflagly
gwvyhafvaaywsndgggstalrwgmigflgseiatfgagfayyffiragtqwstaasaipdgflgslvvvntailvvss
ftlHFAHvalrkgnrsrflallvstlvlgvvfiggqvyeyyefiahegftlsgglfesaffgltglHGLHvtmgavligi
imvrglrgqysadrhtsvstvsmywhfvdivwiflvvvlyagsva

sionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ShortRead_1.14.4     latticeExtra_0.6-24  RColorBrewer_1.0-5
[4] Rsamtools_1.8.6      lattice_0.20-6       Biostrings_2.24.1
[7] GenomicRanges_1.8.13 IRanges_1.14.4       BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] Biobase_2.16.0 bitops_1.0-5   grid_2.15.1    hwriter_1.3
[5] stats4_2.15.1  tools_2.15.1   zlibbioc_1.2.0

thank you very much
--
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu
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