User: kevin.l.neff

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kevin.l.neff240
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Mayo Clinic College of Medicine
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7 years, 5 months ago
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7 years, 6 months ago
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Posts by kevin.l.neff

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Blast Settings For Short Sequences
... http://www.ncbi.nlm.nih.gov/BLAST/Why.shtml You can adjust both the word size and the expect value on the standard BLAST pages to work with short sequences. However, we do provide a BLAST page with these values preset to give optimum results with short sequences. This page ("Search for short and ne ...
written 7.5 years ago by kevin.l.neff240
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Comment: C: Turn Off Blast Search On Reverse Complement Strand In Blastn
... I'm not sure this option even works because it's giving me identical results for plus and minus. ...
written 7.5 years ago by kevin.l.neff240
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Answer: A: Turn Off Blast Search On Reverse Complement Strand In Blastn
... For BLAST+, it's -strand {both,plus,minus} ...
written 7.5 years ago by kevin.l.neff240
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Answer: A: Blast Settings For Short Sequences
... oh, the option -task "blastn-short" seems to do the trick. Only works for queries equal to or longer than 17 bases.... I wish this stuff was documented somewhere. This task is mentioned in the command-line manual, but nothing about its settings. ...
written 7.5 years ago by kevin.l.neff240
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Blast Settings For Short Sequences
... I'm searching for short sequences in nt. By short, I mean 10-20 bases. When I run blastn, I get no results, regardless of my -evalue settings. Here's the test sequence: >ponzr CGCGGTAAAACACATTTG And I run BLAST as follows: ./blastn -db nt -remote -query test2.seq -task "megablast" -out tes ...
blast written 7.5 years ago by kevin.l.neff240 • updated 11 months ago by friist10
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Answer: A: Blast Execution Problem
... make sure you have nr.nal in the current directory or specify it at the command line. I think you can say -db ./db/nt or something like that. ...
written 7.5 years ago by kevin.l.neff240
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Comment: C: Species-Specific Output From Blast -Db Nt -Remote ...
... Yes, I agree. However, my web server only allows 10 GB data, so I need to come up with an alternative. Dreamhost or some other service may be the easiest solution, but I wondered if there was a way to do this without bringing in the big guns. Seems like no... ...
written 7.5 years ago by kevin.l.neff240
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Comment: C: Species-Specific Output From Blast -Db Nt -Remote ...
... http://www.biostars.org/post/show/15002/make-a-custom-blast-library-using-the-output-of-another-blast-result/#45602 ...
written 7.5 years ago by kevin.l.neff240
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Comment: C: Species-Specific Output From Blast -Db Nt -Remote ...
... Sadly, this doesn't work with -remote option. ...
written 7.5 years ago by kevin.l.neff240
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Species-Specific Output From Blast -Db Nt -Remote ...
... I'm using the C++ version of blastn, with -db nt and -remote. I need to limit my search to a specific organism. I've had success using -gilist <file> to do this on searches with a local database, but that option is excluded for remote searches. Should I use a script to filter the search res ...
blast written 7.5 years ago by kevin.l.neff240 • updated 5.3 years ago by chris.mit760

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