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Question: BLAST E-value
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gravatar for Alla Bulashevska
7.8 years ago by
Alla Bulashevska60 wrote:
Dear Bioconductor users, i am doing cross-species analysis and searching for the way how to pairwise align thousands of sequences efficiently. I should become the BLAST E-value as output. The pairwiseAlignment in the Biostrings package can align two protein sequences but outputs Smith Watermann score. I will appreciate it greatly if somebody can tell me, how this score could be transferred into E-value. Thank you for your help, Alla.
ADD COMMENTlink modified 7.8 years ago by Richard Friedman2.0k • written 7.8 years ago by Alla Bulashevska60
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gravatar for Richard Friedman
7.8 years ago by
Richard Friedman2.0k wrote:
Dear Alla, I am not acquainted with biostrings but the E value is not a function of a single alignment. It is a function of an entire database search. It is the number of sequences in the database with the same score or higher by chance. Therefore there cannot be an E-value for a single pairwise alignment. I can send you some instructional material from my course that deals with this issue off line if that would be helpful. Best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, Patrick McGoohan On Feb 16, 2010, at 1:36 PM, Alla Bulashevska wrote: > > Dear Bioconductor users, > i am doing cross-species analysis and searching for the way > how to pairwise align thousands of sequences efficiently. I > should become the BLAST E-value as output. > The pairwiseAlignment in the Biostrings package can align > two protein sequences but outputs Smith Watermann score. > I will appreciate it greatly if somebody can tell me, how > this score could be transferred into E-value. > > Thank you for your help, > Alla. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.8 years ago by Richard Friedman2.0k
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gravatar for michael watson IAH-C
7.8 years ago by
michael watson IAH-C3.4k wrote:
Have you tried the bl2seq program from NCBI? ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Alla Bulashevska [alla.bullashevska@fdm.uni-freiburg.de] Sent: 16 February 2010 18:36 To: bioconductor at stat.math.ethz.ch Subject: [BioC] BLAST E-value Dear Bioconductor users, i am doing cross-species analysis and searching for the way how to pairwise align thousands of sequences efficiently. I should become the BLAST E-value as output. The pairwiseAlignment in the Biostrings package can align two protein sequences but outputs Smith Watermann score. I will appreciate it greatly if somebody can tell me, how this score could be transferred into E-value. Thank you for your help, Alla. _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.8 years ago by michael watson IAH-C3.4k
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/bl2seq.html This does indeed provide a BLAST e-value. ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of michael watson (IAH-C) [michael.watson@bbsrc.ac.uk] Sent: 17 February 2010 22:44 To: Alla Bulashevska; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] BLAST E-value Have you tried the bl2seq program from NCBI? ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Alla Bulashevska [alla.bullashevska@fdm.uni-freiburg.de] Sent: 16 February 2010 18:36 To: bioconductor at stat.math.ethz.ch Subject: [BioC] BLAST E-value Dear Bioconductor users, i am doing cross-species analysis and searching for the way how to pairwise align thousands of sequences efficiently. I should become the BLAST E-value as output. The pairwiseAlignment in the Biostrings package can align two protein sequences but outputs Smith Watermann score. I will appreciate it greatly if somebody can tell me, how this score could be transferred into E-value. Thank you for your help, Alla. _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.8 years ago by michael watson IAH-C3.4k
Dear Alla, Both Richard and Michael have a similar idea to me but to elaborate on their ideas a little. I am not sure your exact biological question but say, for instance, your species are rat and mouse. 1) download the command line version of NCBI blast and install it http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DO C_TYPE=Download 2) (assuming your proteins are in FASTA format) use the formatdb command to format your rat proteins into A BLAST-able database formatdb -i rat_proteins -n rat_proteins -o T -p T 3) run BLAST pairwise sequence alignment algorithm by searching the mouse proteins against your rat protein database. Use this command: blastall -p blastp -i mouse_proteins -d rat_proteins -e 0.01 -o mouse_vs_rat_proteins The file mouse_vs_rat_proteins will contain each mouse protein as a query against the database of rat proteins, which will include an alignment and an e-value for each. You can just type blastall to see the different command line arguments, where you can change output formats and restrict the number of hits reported etc. You may want a perl parser to process your blast output to make sense of all the alignments (you say you have thousands of proteins). If you are interested in ortholog relationships between species, I wrote a simple pipeline that uses a Conditional Stepped Reciprocal Best Hit approach to infer ortholog relationships between model and non-model species. http://www.biomedcentral.com/1471-2164/10/490 If you want to use that, email me personally and I will see if it is a appropriate to your data and biological question. I hope that helps. Kind regards, John. -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of michael watson (IAH-C) Sent: 17 February 2010 22:56 To: michael watson (IAH-C); Alla Bulashevska; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] BLAST E-value http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/bl2seq.html This does indeed provide a BLAST e-value. ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of michael watson (IAH-C) [michael.watson@bbsrc.ac.uk] Sent: 17 February 2010 22:44 To: Alla Bulashevska; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] BLAST E-value Have you tried the bl2seq program from NCBI? ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Alla Bulashevska [alla.bullashevska@fdm.uni-freiburg.de] Sent: 16 February 2010 18:36 To: bioconductor at stat.math.ethz.ch Subject: [BioC] BLAST E-value Dear Bioconductor users, i am doing cross-species analysis and searching for the way how to pairwise align thousands of sequences efficiently. I should become the BLAST E-value as output. The pairwiseAlignment in the Biostrings package can align two protein sequences but outputs Smith Watermann score. I will appreciate it greatly if somebody can tell me, how this score could be transferred into E-value. Thank you for your help, Alla. _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.8 years ago by John Herbert80
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