Question: Archieve of homologous nucleotide sequence across genome
0
gravatar for CY
11 months ago by
CY510
United States
CY510 wrote:

I am looking for any reference file that archieves homologous nucleotide sequence (homologous gene) across genome. It could a file harbored in FTP site, a database or a tool for that. Does anyone have any recommendation?

P.S. For clarification, what I would like to get is a list of genes or regions (in human genome) that have similar (homologous) sequences (in human genome). For example, gene ABC1, ABC2 and ABC3 (assuming these are ABC homologs and share similar nucleotide sequence). It would be preferable if I can get a list like this directly. Alternatively, I can use tools such as biopython BLAST E-util or ClustalW to make such list. However, this is a new field to me and I have no idea how should I proceed.

sequence • 238 views
ADD COMMENTlink modified 11 months ago by juanjo75es70 • written 11 months ago by CY510
1

NCBI Homologene, UCSC multi-genome comparisons (example for human, others available, look in pairwise and multiple alignments) and Ensembl Compara.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax87k
0
gravatar for h.mon
11 months ago by
h.mon30k
Brazil
h.mon30k wrote:

OrthoDB and OMA Orthology Database, among others, have the information you want.

ADD COMMENTlink written 11 months ago by h.mon30k

Sorry for confusion. What I meant is to get the homologous genes / regions across human genome.

ADD REPLYlink written 11 months ago by CY510

You could start by looking for paralogs. You can find them in Ensembl using the compara API or BioMart.

ADD REPLYlink written 11 months ago by Jean-Karim Heriche23k
0
gravatar for juanjo75es
11 months ago by
juanjo75es70
juanjo75es70 wrote:

Apart from BLAST you can now try that link. It makes use of a different technology and looks for homolog matches with the same length instead of submatches as BLAST does.

ADD COMMENTlink written 11 months ago by juanjo75es70
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