[Biopython] Fetching fasta sequences by accession number

[Iddo Friedberg]

You can use the Uniprot REST API: http://www.uniprot.org/help/api_queries

On Sat, Apr 21, 2018 at 3:02 PM, Ahmad Abdelzaher <underoath006 at gmail.com>
wrote:

> Thanks a lot. I actually coded it and only after running, I realized I was
> misinformed. I don't have the accession numbers, I have gene names like
> this HS71L_HUMAN, CATIP_HUMAN , ZMY12_HUMAN, ..etc. Any suggestions?
>
> Regards.
>
> On Fri, Apr 20, 2018 at 2:44 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>
>> Uniprot has several APIs to access it: http://www.uniprot.org/help/pr
>> ogrammatic_access but I am not sure there is a module in biopython that
>> accesses that. But it should be easy to do, just use a script to retrieve
>> this generic URL:
>>
>> https://www.uniprot.org/uniprot/P12345.fasta
>>
>> where "P12345" is replaced by whatever UniprotID you have.
>>
>>
>> Then you can upload your concatenated FASTA file to the HMMER site, I am
>> not sure what their size limitation is.
>>
>> If it's only swissprot you are interested in, and you have the disk
>> space, I suggest you download it, download HMMER and whatever reference
>> databases you wish to run against, and do it all locally. Especially if you
>> have a large number of sequences to process. Biopython can read swissprot
>> or XML uniprot files via SeqIO.
>>
>> To download uniprot: http://www.uniprot.org/downloads
>>
>>
>> On Fri, Apr 20, 2018 at 1:11 PM, Ahmad Abdelzaher <underoath006 at gmail.com
>> > wrote:
>>
>>> Thank you for the reply. The accession numbers that I want to fetch the
>>> fasta sequences for are uniprot accession numbers. I want to search for
>>> homologs for these sequences on HMMR: https://www.ebi.ac.uk/Tools/hmmer/
>>>
>>> Any suggestions on how to do so?
>>>
>>> On Fri, Apr 20, 2018 at 10:16 AM, Iddo Friedberg <idoerg at gmail.com>
>>> wrote:
>>>
>>>> There is an example here for downloading multiple GenBank entries:
>>>> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc131
>>>>
>>>> Depending on the actual database you are downloading from, you can use
>>>> rettype="fasta" or convert a genbank file to fasta as in here:
>>>> http://biopython.org/wiki/Converting_sequence_files
>>>>
>>>> The possible rettype and retmode  are  dependent on the database you
>>>> are fetching from, and determined of the efetch API . More about that
>>>> here:  https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
>>>>
>>>> HTH,
>>>>
>>>> Iddo
>>>>
>>>>
>>>> On Fri, Apr 20, 2018 at 6:25 AM, Ahmad Abdelzaher <
>>>> underoath006 at gmail.com> wrote:
>>>>
>>>>> How can I batch download fasta sequences by accession number? Is there
>>>>> a Biopython method that can do that? Any other suggestions or alternatives?
>>>>>
>>>>> Regards.
>>>>>
>>>>> _______________________________________________
>>>>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>>>>> http://mailman.open-bio.org/mailman/listinfo/biopython
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Iddo Friedberg
>>>> http://iddo-friedberg.net/contact.html
>>>> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
>>>> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
>>>> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>>> >>----.<--.>++++++.<<<<------------------------------------.
>>>>
>>>
>>>
>>
>>
>> --
>> Iddo Friedberg
>> http://iddo-friedberg.net/contact.html
>> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
>> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
>> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>> >>----.<--.>++++++.<<<<------------------------------------.
>>
>
>


-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>----.<--.>++++++.<<<<------------------------------------.
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