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Questions tagged [blastn]

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Find indels between two short sequences

I have two sequences, say AAAGCTCGAGG and AAAGCGAGG. I need a convenient tool which shows me insertions or deletions between these, i.e. in this case something like ...
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1answer
20 views

blast nt vs Genbank

What is the difference between these two databases? ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and ftp://ftp.ncbi.nih.gov/genbank/ I understand that BLAST database has both nt for nucleotide and np for ...
1
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1answer
50 views

Plotting distance tree from blastn output

I'm trying to plot a simple distance tree of my blastn output with nj (like the tree view on NCBI). From what I understood, what I think I should do is extract all the hsps from each alignment re-...
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2answers
32 views

Inferring a phylogenetic tree from BLASTn

I am trying to infer a phylogenetic tree from a Blastn output and from what I have understood, what I should do is 1) extract the alignments and re-align them using Muscle, then 2) feed the .aln file ...
2
votes
1answer
66 views

Appropriate tool or algorithm for sloppy alignment of degenerate bases

I have an optimization problem where I have a degenerate nucleotide sequence I want to align against subsets of a reference genome (exons, specifically, to make the problem more tractable). The ...