O'Reilly logo

Beginning Perl for Bioinformatics by James Tisdall

Stay ahead with the world's most comprehensive technology and business learning platform.

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, tutorials, and more.

Start Free Trial

No credit card required

BLAST Output Files

The following is part of a BLAST output file. I created it by entering a few lines of the sample.dna file from Chapter 8 into the BLAST program at the NCBI web site, without changing any of the default parameters. I then saved the output as text in the file blst.txt, which is available from this book's web site. I've used it repeatedly in the parsing routines throughout this chapter. Because the output is several pages long, I've truncated it here to show the beginning, the middle, and the end of the file.

BLASTN 2.1.3 [Apr-11-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. RID: 991533563-27495-9092 Query= (400 letters) Database: nt 868,831 sequences; 3,298,558,333 total letters Score E Sequences producing significant alignments: (bits) Value dbj|AB031069.1|AB031069 Homo sapiens PCCX1 mRNA for protein cont... 793 0.0 ref|NM_014593.1| Homo sapiens CpG binding protein (CGBP), mRNA 779 0.0 gb|AF149758.1|AF149758 Homo sapiens CpG binding protein (CGBP) m... 779 0.0 ref|XM_008699.3| Homo sapiens CpG binding protein (CGBP), mRNA 765 0.0 emb|AL136862.1|HSM801830 Homo sapiens mRNA; cDNA DKFZp434F174 (f... 450 e-124 emb|AJ132339.1|HSA132339 Homo sapiens CpG island sequence, subcl... 446 e-123 emb|AJ236590.1|HSA236590 Homo sapiens chromosome 18 CpG island ...

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, interactive tutorials, and more.

Start Free Trial

No credit card required