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Forum: Bioinformatics 07-05-2014, 06:16 PM
Replies: 3
Views: 946
Posted By emanlee
Thanks. For the well-studied organisms, there are...

Thanks. For the well-studied organisms, there are multiple alignments. We can get phastcons and take them as conservation levels. For others, such as Alpaca genome, there are only pairwise alignments...
Forum: Bioinformatics 07-05-2014, 12:46 AM
Replies: 3
Views: 946
Posted By emanlee
Smile Is there a way to determine the conservation of any genomic regions?

We identified a long intergenic non-coding RNA in chicken, for example, located:
exon1, chr1, 200000,201000,+
exon2, chr1, 203000,204000,+
Is there a way to determine conservation levels across...
Forum: Bioinformatics 07-03-2014, 05:09 AM
Replies: 3
Views: 1,819
Posted By emanlee
Thanks! We are not sure what hash code were used...

Thanks! We are not sure what hash code were used in Runhash and Readhash.
We have seen such a post:
http://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Run_
Forum: Bioinformatics 07-02-2014, 07:33 PM
Replies: 3
Views: 1,819
Posted By emanlee
Smile md5sum got different hash code of SRA files

Hi, All
We downloaded ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR308/SRR308015/SRR308015.sra
and check its md5sum using the following command on linux:
md5sum...
Forum: Bioinformatics 06-04-2014, 03:30 AM
Replies: 1
Views: 1,048
Posted By emanlee
Sorry, I just got it: - full length...

Sorry, I just got it:

- full length protein-coding -> the protein-coding transcripts that have no "cds_start_NF" or "cds_end_NF" tag
- partial length protein-coding: -> all the rest (they...
Forum: Bioinformatics 06-04-2014, 03:09 AM
Replies: 1
Views: 1,048
Posted By emanlee
Question Can we extract full-length trascripts from gencode gtf

Hello, all

We can see that GENCODE released statistics and GTF annotation as follows:

(1) Statistics: (extracted gencode V19 from : http://www.gencodegenes.org/stats.html )
...
Forum: Bioinformatics 05-26-2014, 05:44 AM
Replies: 0
Views: 1,032
Posted By emanlee
Question How to get mouse multiple sequence alignments in fasta format

There are compressed multiple alignments of 59 assemblies to the mouse genome (mm10/GRCm38, Dec. 2011)
Readme and directory:
http://hgdownload-test.sdsc.edu/goldenPath/mm10/multiz60way/
MAF files:...
Forum: Bioinformatics 05-22-2014, 06:19 PM
Replies: 0
Views: 1,422
Posted By emanlee
Smile how to feed de novo assembled transcripts to PhyloCSF

We have human de novo assembled transcripts. Those transcripts were assembled de novo without human genomic by using Trinity/Newbler. We want to use PhyloCSF to identify coding or noncoding...
Forum: Bioinformatics 05-19-2014, 06:07 PM
Replies: 4
Views: 1,103
Posted By emanlee
REF: ...

REF:
http://generic-model-organism-system-database.450254.n5.nabble.com/Getting-gbrowse-syn-to-work-with-MySQL-td5519255.html
Forum: Bioinformatics 05-19-2014, 02:53 PM
Replies: 4
Views: 1,103
Posted By emanlee
What is between "use Bio:" and "B::GFF;" in the...

What is between "use Bio:" and "B::GFF;" in the perl script "use Bio: icon B::GFF;" ?
Forum: Bioinformatics 05-17-2014, 11:19 PM
Replies: 3
Views: 4,194
Posted By emanlee
Another thread on this issue: ...

Another thread on this issue:
http://seqanswers.com/forums/showthread.php?t=5224

A solution based on mgogol's code:
https://sourceforge.net/projects/collapsefpkm/files/?source=navbar
Forum: Bioinformatics 05-17-2014, 09:10 PM
Replies: 26
Views: 15,328
Posted By emanlee
Smile Collapse duplicate FPKMs for a gene

The format of cufflinks outputs (genes.fpkm_tracking files) are now different from previous. I updated the code written by mgogol and published it on sourceforge.net...
Forum: Bioinformatics 09-22-2013, 04:38 PM
Replies: 7
Views: 4,162
Posted By emanlee
>>> from Bio import SeqIO >>> count =...

>>> from Bio import SeqIO
>>> count = SeqIO.convert("uniref90.xml", "uniprot-xml", "uniref90converted.fasta", "fasta")
>>> print("Converted %i records" % count)
Converted 0 records

We checked...
Forum: Bioinformatics 09-22-2013, 05:43 AM
Replies: 7
Views: 4,162
Posted By emanlee
Thank you for your quick reply. I'll try it out.

Thank you for your quick reply. I'll try it out.
Forum: Bioinformatics 09-22-2013, 03:09 AM
Replies: 7
Views: 4,162
Posted By emanlee
format uniref90.xml to database for BLAST

we want to get a formated database for BLAST from Uniref90.
we referred an article which used an early release Uniref90, say version 10.0
ftp.uniprot.org only provide the XML format of this...
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