User: andytsaica

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andytsaica0
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Posts by andytsaica

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How do I find cross-reactive species given two primers?
... I have developed my own algorithm to find two 15-nt long primers for a specific gene. I now want to search NCBI primer-blast to see what organisms those two primers that I want to use will cross-react with. What search parameters do I use on primer-blast in order to do this? ...
bioinformatics blast primer written 3.3 years ago by andytsaica0 • updated 3.1 years ago by Biostar ♦♦ 20
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Comment: C: Short Sequence BLAST Search with Gaps
... I didn't put any command, the results just ended up being on 100% identity matches using the settings that I posted above. ...
written 3.3 years ago by andytsaica0
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Comment: C: Short Sequence BLAST Search with Gaps
... I am blasting against the entire nt database. I have tried making gap open penalty 0, and gap extension penalty the lowest it can be, but that still doesn't help. ...
written 3.3 years ago by andytsaica0
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Comment: C: Short Sequence BLAST Search with Gaps
... I have tried fooling around with the gap penalties, but there are still only 100% matches. I have a feeling that 15 nucleotides may be too short to find sequences gaps within a reasonable number of hits since there are so many hits. When I do a sequence of ~35 nucleotides, then several gaps start sh ...
written 3.3 years ago by andytsaica0
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Short Sequence BLAST Search with Gaps
... I am running a BLASTN search on a 15-nucleotide sequence with the following parameters: expect threshold = 1000, word size = 7, match/mismatch = 1, -3, no filters or masks I am getting only 100% identity hits. However, I am also interested in hits with mismatches or gaps in the middle of the seque ...
gaps short alignment blast written 3.3 years ago by andytsaica0 • updated 3.3 years ago by Michael Dondrup44k

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