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The results were output in the BLAST file format.
The entire BLAST file can also be examined through POPE's tables.
A BLASTp analysis was applied to the resulting concatenated file against itself, with an e-value of 10−20, to generate an all-vs-all BLAST file.
The results from these A vs. B and B vs. A analyses were combined to produced a single A-B blast file.
The BLAST file and gff file were imported for synteny block analysis according to the procedure described in the manual of MCScanX.
The all-vs-all BLAST file was loaded into the databases of orthoMCL and the sequences were clustered with the MCL software to generate the final groups of orthologous genes.
Similar(53)
The blast files were imported into MEGAN using the import option BLASTN.
The two BLAST files were combined in order to keep information obtained in both BLASTX analyses.
The results from these analyses were combined to produce a melon-cucumber and a melon-watermelon blast files.
CTG genes with top database hits to bacterial species were identified as putative horizontally transferred genes and the resultant Blast files were inspected manually.
Perl scripts were used to retrieve information from the Blast output files (see Additional file 2, scripts 2 and 3).
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