Question: Website that provides fasta sequences from Gene ID
0
gravatar for ksi216
2.4 years ago by
ksi21640
ksi21640 wrote:

I was wondering if there was a website or tool I can get fasta sequences from a bunch of Gene ids?

geneid blast bioinformatics • 1.0k views
ADD COMMENTlink modified 2.4 years ago by genomax55k • written 2.4 years ago by ksi21640
1
gravatar for genomax
2.4 years ago by
genomax55k
United States
genomax55k wrote:

Are the ID's from a single organism? If so you could use BioMart on the relevant genome page at Ensembl or Table Browser tool at UCSC (if the genome is available from either location).
Not a web site based solution: but if those are NCBI ID's (can be from many organisms) then you could use blastdbcmd tool from Blast+ suite and nt/nr blast indexes to retrieve fasta sequences.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by genomax55k

they are Gene Ids from the human CCDS file from NCBI , they will be from the same chromosome. Sorry I didn't specify. So in that case is BioMart my best option ?

ADD REPLYlink written 2.4 years ago by ksi21640

the reason I need the fasta sequences is to blast the corresponding sequences from the Gene Ids, if only we could run a blast using the GENE id

ADD REPLYlink written 2.4 years ago by ksi21640

Web Blast @NCBI will accept accession numbers/gi so you could use Uniprot ID converter to convert your gene ID's to those.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax55k

As I mentioned with my comment before, a lot of things get simplified in this thread to a point where it is just wrong, so I have to say something. Blast is not accepting accession numbers. Blast is an algorithm. There are different implementations of this algorithm on different websites and tools. But Blast does not accept anything. In your own interest, be more careful with the wording and meaning of terms - and also read a bit about the background of the methods instead of just 'using' it - it will help in the long run.

ADD REPLYlink written 2.4 years ago by LLTommy1.2k

Since the discussion was about websites Blast I was referring to was @NCBI. I have clarified my post above to include that information.

ADD REPLYlink written 2.4 years ago by genomax55k

how do i do that ? is there a link on bioperl ?

ADD REPLYlink written 2.3 years ago by ksi21640

You can put CCDS IDs into Ensembl BLAST.

ADD REPLYlink written 2.4 years ago by Emily_Ensembl15k

I think that genomax2 touched an important point here, and obviously what I was thinking right away - so ks216: What is a gene id? Where do you get your id's from? There is not a world wide unique id for everything. You have to ask yourself some more questions and understand the complexity of bioinformatics and its services.

ADD REPLYlink written 2.4 years ago by LLTommy1.2k

I am new to this, I was under the impression that the Gene Ids were unique, but that's not the case. I understand that blast is an algorithm. thank you all for your help.

ADD REPLYlink written 2.4 years ago by ksi21640

Hey, it is ok that you are new to this, don't get me wrong. All I try is to open your eyes a little bit. There are many many services and many many different databases . There often is not one solution, but many. Often it is not clear what the best solution is, rather you have to test some and find out yourself what works best for your experiment. This is truly a real challenge in bioinformatics and that is why I want to help you to understand this. So keep that in mind in the future.

ADD REPLYlink written 2.4 years ago by LLTommy1.2k

how do i use the blastdbcmd from bioperl i didnt see a tutorial

ADD REPLYlink written 2.3 years ago by ksi21640
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