SeqAnswers portal 06-10-2014d1446

2015-05-06

SeqAnswers portal 06-10-2014d1446
bioinformatics forum

http://seqanswers.com

Some posts
-question about program to automatically annotate a DNA sequence
--http://seqanswers.com/forums/showthread.php?s=c7bb55794f5bd9a0a7212cc418074f51&p=143952#post143952
--they suggested Blast2GO
---I emailed someone at Blast2Go
{
question about whether blast2go can annotate chimeric transcripts
-email
{
Subject: 	Re: [#1873] Re: chimeric transcripts?
From: 	Mariana Monteiro (support@blast2go.com)
To: 	azim58@yahoo.com;
Date: 	Wednesday, July 2, 2014 2:22 PM 
}
--
{
Dear support,
Blast2GO uses sequence alignments (Blast) as well as protein domains/sites (InterProScan) to transfer Gene Ontology functions from characterized proteins to novel sequences.
In the case of chimeric transcripts I would guess that Blast will not produce significant alignments sufficient for function transfer. However, with some InterProScan algorithms it might be possible to find sites which correspond to a region of one of the "chimeric exons" and this could have a certain impact on the whole transcript. Please consider this just as an educated guess from my site. This is something which you could test with Blast2GO to further evaluate the results.  
Best regards,
Stefan
}
}
-question about displaying the orientation of sequences in an alignment
--http://seqanswers.com/forums/showthread.php?p=143606#post143606
--they said JBrowse can do it, but they said it is difficult to setup
-there were many other replies as well
-program to automatically annotate a DNA sequence 06-27-2014d1552
--http://seqanswers.com/forums/showthread.php?p=143795#post143795
{
Is there some good software to automatically annotate a DNA sequence?  I'm dealing with a specific situation right now, but it would be nice to have a general tool that just takes a DNA sequence and automatically annotates it well based on information from databases.  In my situation right now, I am looking at chimeric transcripts in cancer cells where two transcripts from different genes are fused together.  Therefore, I get a sequence, blast it, find out which part matches with transcript A, find out which part matches with transcript B, and then I annotate it using APE (Advanced Plasmid Editor) to mark which part of the sequence corresponds to transcript A and B, the start codon, the stop codon.  I can then acquire some useful information such as the protein produced, and the protein sequence after the fusion point.  Anyway, does anyone have a good recommendation for automatically annotating DNA sequences?
}
-display orientation of sequences in alignment
--http://seqanswers.com/forums/showthread.php?p=142582#post142582
{
How can I display the orientation of sequences in a blast alignment?  In particular, I am using Bl2seq to align multiple sequencing results and primers, and I would like to be able to quickly see the orientation of the aligned sequences and primers.  Is there a way to do this from the BLAST website.  Is there some other tool that will do this (preferably a free one)?
}

See also
-[pr_SeqAnswers account 06-10-2014d1447]

azim58wiki: