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
