blast.py is a remote BLAST wrapper written in Python2.7 capable of running multiple parallel instances of remote BLAST searches

blast.py has several options (see below) that allow you to costumize your BLAST searches. Here I will present just a few examples:

• blast.py -in INPUTFILE -o OUTPUTFILE_NAME

Here, the "-in" option is used to specify the FASTA input file name, and the "-o" option is used to specify the name of the BLAST output file. By default, blast.py will run the "blastn" program on the "NR" database and the output will be in "XML" format. It will use an e-value threshold of "1" and will limit the number of best hits per search to "50". Seven parallel instances will be run, as in BLAST2GO. I do not advise you to use a larger number because it may causa overload of the remote servers, resulting in a severed connection. All these options can be changed using the options below.

• blast.py -in INPUTFILE -b blastp -db swissprot -o OUTPUTFILE_NAME

Here, I specified the "blastp" program and swissprot database, instead of the default "blastn" and "nr".

• blast.py -in INPUTFILE -b tblastn -e 1e-10 -o OUTPUTFILE_NAME

Here, I specified the "tblastn" program and an evalue cut off of 1e-10

Since this program depends on the good will of the NCBI servers, I also implemented a fail safe in case the connection is lost. When the program detects that the BLAST search was not completed for any reason, it will produce a new FASTA file (that will end with ".resume") containing the sequences that were not BLASTed yet. In this way, the user can resume the BLAST search from the last saved point, avoiding the inconveniance of having to start all over again and BLASTing sequences repeatedly.

Depending on you internet connection, this is not a common issue (happened only once in my tests), but I implemented this nevertheless, just to be on the safe side.

blast.py has the following options (which can also be consulted by typing "blast.py -h" or "blast.py --help" in the command line):

-h, --help show this help message and exit

-in INFILE Provide the FASTA input file name

-b {blastn,blastp,blastx,tblastn,tblastx} Select the BLAST program to run (default is 'blastn')

-db DATABASE Select the data base to run BLAST (default is 'nr')

-e EVALUE The minimum e-value. Notation can be '0.001' or '1e-3' (default is '1')

-hit HITLIST The maximum number of hits per BLAST search (default is '50')

-p PROC The number of parallel instaces to run BLAST. Use with caution, as a number larger than 7 may cause the connection to be severed due to overload

-o OUTPUTFILE Please provide the name of the output file

-outfmt {HTML,Text,ASN.1,XML} Select the BLAST output format