blast'n'bury - BLAST your sequences and bury them in a database
blastnbury.pl [-q] [-noblast] [-hit -report -save]
blastnbury takes a fasta file of DNA sequences and BLASTs them against nt, followed by saving each resulting BLAST report into a tab-separated file (.txt). The script then loops through the files extracting relevant information, and presents them to the user. The user then decides which of the "best" hits are saved. The selected results of all sequences are then exported to a CSV file.
- -q
-
FASTA file of DNA sequence(s). Sequence names (headers) have to be formatted in the following way:
>AAA_BBBB_CCC, where
AAA = sequence prefix (e.g. organism, collection, experiment).
BBBB= sequence code (e.g. number, strain code).
CCC = genetic region (e.g. 18S, 28S, ITS, CO1).
- -noblast
-
No remote BLAST is performed. For analysing existing BLAST reports.
- -hit
-
Number of BLAST hits per sequence that are saved in tab-delimited files (default: 100)
- -report
-
Number of "best" sorted Blast hits from which the user can choose (default: 15)
- -save
-
Number of "best" sorted Blast hits the user can choose for the CSV file (default: 5). Do not change w/o telling OSIRIS.
- -man
-
Prints the manual page and exits.
Dominik R. Laetsch, dominik.laetsch@gmail.com