Iterative HMMER search algorithm
- pandas
- numpy
- Bio
- matplotlib
- progressbar
- HMMER suite
You will need a protein database to search against. We recommend you use TREMBL. The database needs to be in the FASTA format.
You can download TREMBL from this ftp: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
Informations here: https://www.uniprot.org/downloads
You will need an alignement to draw from such that we can build HMM with the rolling window. The alignment must be in FASTA.
Options:
-h, --help show this help message and exit
-a ALIGNPATH, --alignment=ALIGNPATH
[Required] Location of the FASTA alignement file.
-w WINDOW, --window=WINDOW
[Required] Size of the sliding window (aka minimum nb
of columns to be used for HMM generation)
-n NAME, --name=NAME [Required] Name of the analysis)
-l, --analyze [Optional] Analyze only)
-d DB, --db=DB Path to DB (default to Trembl)
-o, --oskar Is it the Oskar Gene ?
-p, --preprocess Do not preprocess the search. (slower and more prone
to false positives)