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