From fritz.franz at gmx.net Thu Oct 27 23:19:37 2016 From: fritz.franz at gmx.net (fritz.franz at gmx.net) Date: Thu, 27 Oct 2016 23:19:37 +0200 Subject: [Inparanoid] BLAST score Message-ID: An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Fri Oct 28 14:03:02 2016 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Fri, 28 Oct 2016 14:03:02 +0200 Subject: [Inparanoid] BLAST score In-Reply-To: References: Message-ID: <58133E76.1050404@scilifelab.se> Hi Fritz, yes the score depends on blast options such as score matrix adjustment. You can see the used options in the inparanoid.pl script. Erik On 2016-10-27 23:19, fritz.franz at gmx.net wrote: > Hi everybody, > I have a question concerning the BLAST scores in InParanoid8. I > realized that the BLAST scores are pretty different from the scores I > get in a standard BLAST search at blast.ncbi.nlm.nih.gov > . I assume that InParanoid automated > BLAST searches use a different set of BLAST scoring parameters than > standard. Do you know what the settings are? Or is there a different > reason why the BLAST scores are different? > Thank you very much for your help! > Fritz Franz > > > _______________________________________________ > InParanoid-at-sbc.su.se mailing list > InParanoid-at-sbc.su.se at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From fritz.franz at gmx.net Sat Oct 29 11:54:00 2016 From: fritz.franz at gmx.net (fritz.franz at gmx.net) Date: Sat, 29 Oct 2016 11:54:00 +0200 Subject: [Inparanoid] INPARANOID BLAST search Message-ID: An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Mon Oct 31 11:53:40 2016 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 31 Oct 2016 11:53:40 +0100 Subject: [Inparanoid] INPARANOID BLAST search In-Reply-To: References: Message-ID: <6acad1bf-970c-5140-f8f2-189cddc36b1b@scilifelab.se> Hi, that is just a regular Blast search to find the protein you are looking for. Erik On 10/29/2016 11:54 AM, fritz.franz at gmx.net wrote: > Hi, > I have a question concerning the InParanoid8 Blast search option on > the web page. > Is this just a regular BLAST search or is this already somehow using > the Inparanoid algorithm or a bi-directional Blast search? > I realized that I get different results with the same protein by using > the "Gene search" option and entering the protein ID or by using the > "Blast" option and pasting the protein sequence. According to the FAQ > both options should deliver orthologs. Is this really the case for the > "Blast" option? > Thank you very much for your help! > Fritz > > > _______________________________________________ > InParanoid-at-sbc.su.se mailing list > InParanoid-at-sbc.su.se at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se -------------- next part -------------- An HTML attachment was scrubbed... URL: