Sorry, I should have mentioned earlier, I read the FAQ but still was not clear to me 99% identity.
Can you help me understand? Thanks, Medha _____________________________ -----Original Message----- From: Galt Barber [mailto:[email protected]] Sent: Thursday, July 14, 2011 1:52 PM To: Bhagwat, Medha (NIH/OD/ORS) [E] Cc: '[email protected]' Subject: Re: [Genome] FW: BLAT Identity percent Hi, Medha! Here is how the identity number is calculated: http://genome.ucsc.edu/FAQ/FAQblat#blat4 It includes gaps (or inserts depending on perspective) as well as substitutions. Your blat link shows 2 substitutions, and, on the query side, one insert. -Galt 7/14/2011 7:30 AM, Bhagwat, Medha (NIH/OD/ORS) [E]: > Did I miss the response? Thanks, > > Medha > > > From: Bhagwat, Medha (NIH/OD/ORS) [E] > Sent: Tuesday, July 12, 2011 7:21 PM > To: [email protected] > Cc: Bhagwat, Medha (NIH/OD/ORS) [E] > Subject: BLAT Identity percent > > HI, > > > 1. What does the identity number in the result indicate? > > 2. How it is calculated? > > 3. Example: search against the chimp genome > > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:38694212-38778403&db=panTro3&ss=../trash/hgSs/hgSs_genome_6740_cad6e0.pslx+../trash/hgSs/hgSs_genome_6740_cad6e0.fa&hgsid=202630125> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=38694211&g=htcUserAli&i=../trash/hgSs/hgSs_genome_6740_cad6e0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_6740_cad6e0.fa+NP_000522.3&c=chrX&l=38694211&r=38778403&db=panTro3&hgsid=202630125> > NP_000522.3 837 1 354 354 99.1% X ++ 38694212 > 38778403 84192 > > > > 99.1% identity for the 354 amino acid query should give around 3 mismatches > but has several in the alignment > > > > MLFNLRILLN NAAFRNGHNF MVRNFRCGQP LQNKVQLKGR DLLTLKNFTG EEIKYMLWLS 60 > > ADLKFRIKQK GEylpllqgk slgmifekrs trtrlstetG FALLGGHPCF LTTQDIHLGV 120 > > NESLtDTARV LSSMaDAVLA RVYKQSDLDT LAKEASIPII NGLSDLYHPI QILADYLTLQ 180 > > ehysslkglt lswigdgnni lhsimmsaak fgmhlqaatp kGYEPDASVT KLAEQYAKEN 240 > > GTKLLLTNDP LEAAHGGNVL ITDTWISMGQ EEEKKKRLQA FQGYQVTMKT AKVAASDWTF 300 > > LHCLPRKPEE VDDEVFYSPR SLVFPEAENR KWTIMAVMVS LLTDYSPQLQ KPKF > > > > > Thanks. > > Medha > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
