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Old 07-09-2015, 04:40 PM   #1
TinySci
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Location: Spain

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Default Adding BLAST+ to Python PATH

Very new to bioinformatics and I am trying to write a code that will allow me to use a reference geneset (e.g. MLST) and BLAST it against genomes available on Genbank so that I can create datasets of these genesets.

For example, if I wish to do a multi locus gene comparison for a given genus, I'd like to be able to input my reference gene set, BLAST it against the available genomes and pull the gene sequences (fasta) that match with X% ID from the genome.

The reason I thought to do a BLAST-extraction is because some of the genomes I'm looking through are not annotated.

My idea is to use the BLAST+ tools to do this, but I cannot call the module in python. I've downloaded the software, but can only call it in terminal (I am using a mac). I am using python 2.7.5 and have added numpy and biopython.

Could anyone provide some advice for a novice?

Thanks in advance!
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Old 07-09-2015, 11:02 PM   #2
LeightonP
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Default

There are a number of options open to you. One of which is to use code that others have written and tested (always a decent first option!). BIGSdb may be useful for you (http://pubmlst.org/software/database/bigsdb/). If you have access to a local Galaxy instance, there may be an MLST workflow available to you. If you're using pubMLST-compatible definitions, then this Python script https://github.com/widdowquinn/scrip...cs/run_MLST.py might do what you want, or serve as an example you can build from.
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