1
vote
2answers
37 views
Performing BLAST/SmithWaterman searches directly from my application
Bringing in my questions from stackoverflow:
I'm working on a small application and thinking about integrating BLAST or other local alignment searches into my application. My sear …
1
vote
3answers
64 views
How to perform tRNA sequence alignment (against a domain-specific tRNA covariance models) with COVE (or Infernal) on windows ?
(Sorry for the long header)
Hello all.
I wish to have a FASTA file (or similar) of a tRNA sequences that are aligned.
Here is an example of a FASTA file I would like to align:
…
3
votes
7answers
147 views
What methods do you use for short read mapping?
When it comes to short read mapping there seemingly is no shortage of methods or software to choose from. Yet in practice we found that some published methods did now work at all, …
2
votes
3answers
103 views
How to find a 28bp ‘primer’ sequence in a genome?
Dumb question I know, but...
What tool to use?
I'd like to find forward and reverse primers within an approximate distance of each other... I'd like to accept 1 or two mismatches …
1
vote
3answers
61 views
Computing the reverse and complement of a sequence with Biopython
An example that computes the reverse complement of a sequence with BioPython
#
# Reverse complement example with BioPython
#
from Bio.Seq import Seq
# a separate function to rev …
0
votes
0answers
61 views
Computing the reverse and complement of a sequence with Pygr [closed]
Computing the reverse complement with the Pygr bioinformatics framework:
#
# Reverse complement example with pygr
#
from pygr.sequence import Sequence
# needs a separate functio …
2
votes
1answer
30 views
Score protein variants based on frequency of AA in multiple sequence alignment
For reference, please read this excerpt from
Human non-synonymous SNPs: server and survey
Vasily Ramensky, Peer Bork, and Shamil Sunyaev
Profile analysis of homologous
sequen …
3
votes
3answers
64 views
How to get the sequence of a genomic region from UCSC?
Let's say I want to download the fasta sequence of the region chr1:100000..200000 from the UCSC browser.
How do you do that? I can't find a button to 'export to fasta' in the UCSC …
2
votes
1answer
41 views
Implementation of Blosum62 in the source code of global pairwise alignment of proteins
Hi,
I am trying to implement protein pairwise sequence alignment using "Global Alignment" algorithm by 'Needleman -Wunsch'. I am using VB.NET.
I am not clear about how to includ …
1
vote
6answers
102 views
Where can I get the secondary structure of a protein?
As in the title... I have a protein and I would like to know its secundary structure.
I couldn't find it in uniprot, althought I tought they had annotations for it there.
In the en …
1
vote
1answer
40 views
Genome specific database (Gbrowse / Ensembl type)
I am interested in your opinions about database systems used to store, query and visualize genomic sequence and annotations. I am talking about ca 600-700Mb draft genome with a lar …
1
vote
1answer
35 views
How to validate that a sequence only contains letters from a given alphabet?
How do I verify that a sequence only contains letters from a given alphabet: DNA, RNA, protein?
1
vote
1answer
35 views
Turn off BLAST search on reverse complement strand in blastn
I have a quick question:
How can I turn off search on reverse complement strand of my query nucleotide sequence in blastn?
For example, I don't want 'GUAAAGCCAAAUCUUCGGUUA' to be …
1
vote
3answers
46 views
CHIP DNA deep sequence
Hi, everyone,
I am posting this question for my friend.
He is analyzing his CHIP DNA solid deep sequence data, and find out that near 80% reads can not be mapped to the human genom …
