Files under the /blast/ root directory are listed in Table 2.2.1.
The '_cs' string in HTML, .cgi script, and .REAL program names stands for 'client/server'. They are analogous to those without the '_cs' string in their names. These pages have client/server functionality built-in, allowing them to:
1) make client/server Entrez lookups for query sequences using their gi or accession numbers;
2) search a subset of the selected database through Entrez limit for those databases provided by NCBI; and
3) display blast results in Taxonomy report format for hits from NCBI database.
| Table 2.2.1 Files under blast root directory | |
| File name | File content |
|---|---|
| blast.cgi, blast_cs.cgi | Start-up C-shell script for BLAST searches |
| blast.html, blast_cs.html | Input web form for regular BLAST searches |
| megablast.html, megablast_cs.html | Input web form for MEGABLAST searches |
| rpsblast.html, rpsblast_cs.html | Input web form for RPS BLAST searches |
| blast.rc | Default configuration file for the WWW BLAST server |
| psiblast.rc | Default configuration file for the PSI/PHI-BLAST server |
| psiblast.cgi, psiblast_cs.cgi | Start-up C-shell script for PSI/PHI BLAST searches |
| psiblast.html, psiblast_cs.html | Input web form for PSI/PHI BLAST searches |
| psiblast.REAL, psiblast_cs.REAL | Main PSI/PHI BLAST server executables |
| wblast2.html, wblast2_cs.html | Input web form for 'BLAST 2 sequences' |
| wblast2.REAL, wblast2_cs.REAL | 'BLAST 2 sequences' server executables |
| wblast2.cgi, wblast2_cs.cgi | Start up C-shell script for 'BLAST 2 sequences' |
| bl2bag.cgi | CGI for creating alignment images |
| nph-viewgif.cgi | CGI for viewing and deleting overview images |
| readme.html, readme.txt | Readme for this package |
| wwwblast.log | Default logfile |
| psiblast.log | Default PSI/PHI Blast logfile |
| ncbi_blast.rc | List of common databases available from NCBI |
| index.html | Index page listing the available web forms |
| discontiguous.html | An one page introduction to discontiguous megablast |
| ncbi_blast.rc | Example blast.rc file with NCBI database names |
| config_setup.pl | Script for configuring the database list in the web forms |