Hi All, I have a small db of abut 100 sequencing shorter than 100bp.
I have some really short queries (5-30bp).
When I run blastn with -query myquery -subject mysubject I don't get any matches. I tried reducing the word size using the -word-size option, but still didn't get any matches even though I know they are there.
I know blast is overpowered for my little task, but I am using blast in my program for some other tasks, so it would be easiest if I could just finish it off without using another program.
Also I am using biopython for parsing the blast xml output, so if other program are suggested, please recommend something with a python parser.
thanks!
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Richard
Use Ssearch36 (Smith-Waterman exact local laignments, part of FASTA tools) to get all possible matches. It is feasible with your small dataset. With the -BB option it can mimic blast text output (not XML afaik) quite well, should be good enough to use a blast parser in Bio* libraries to parse this, it worked with BioPerl at least, or you could use the FASTA-output format parser with the standard output format of ssearch. Use of any short-read/heuristic aligner is not an good option in your case, there is no reason to sacrifice accuracy for improving performance if the number of sequences is very small.
You could also use "water" from the EMBOSS package (another Smith-Waterman algorithm implementation). Totally agree on avoiding the heuristics for data sets of this size.
I guess if they are so short then you can try to just use python to detect a 100% match in your database, ie a substring in the database equal to your query. Another option is to use a short read mapper like bowtie2, SHRiMP, or BWA and then parse the output sam or bam files.
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It's not so much that BLAST is "overpowered" in this case, more "inappropriate". Just because you can force it to do short query alignment doesn't mean that's a good idea. Suggest you investigate other alignment tools.