[Bioperl-l] Protein Records without Sequence

[Hamish McWilliam]

No idea how NCBI are planning to handle this. My guess is that the
announcement mentioned in the RefSeq release notes will detail how to
deal with this. Since I cannot find this announcement, I suggest you
contact the RefSeq folks
(http://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi) to see what
their plan is.

FWIW from phrasing of the information in the release notes, it looks
like this may have gone live a bit earlier than originally planned, so
some things may not be in place yet...

All the best,

Hamish

On 5 June 2013 23:10, Warren Gallin <wgallin at ualberta.ca> wrote:
> OK, I see where this is coming from.  If I get a record without the protein sequence I can evaluate it and then retrieve again as a fast file and put it into the Bio::Seq object.
>
> Do you have any idea how they are going to handle this one-to-many mapping?  Given that a single protein sequence may be linked to multiple different nucleotide sequences, even from different species, that means that a single protein sequence record may be tied to several different nucleotide sequence records.
>
> However, when I look up a couple of WP_XXXXXX records, I get the protein sequence but there is no DBSOURCE field, and there is no "coded_by"tag in the feature table so there is no direct way to find the underlying nucleotide sequence(s).
>
> See WP_004062662.1  GI:490164010 as an example.
>
> Is there any current way of retrieving the coding sequence starting from a protein record like this?
>
> Warren Gallin
>
> I am hoping that all of these fields that will now have multiple entries are going to be easily
> On 2013-06-05, at 1:58 PM, Hamish McWilliam <hamish.mcwilliam at bioinfo-user.org.uk> wrote:
>
>> Hi Warren,
>>
>> This is due to a change to the way some entries are handled in the
>> latest RefSeq (protein) data. From the RefSeq release notes
>> (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release59.txt):
>>
>> ---
>>
>> [1] ATTENTION: anticipated change in release 60 or 61
>> The RefSeq project is planning a significant expansion of the
>> prokaryotic dataset.
>> Specifically, NCBI's prokaryotic genome annotation pipeline is
>> generating annotation for all
>> submitted prokaryotic genomes representing strains, disease outbreak
>> sequences, population
>> sequencing, and diversity studies. These genomes include both complete
>> genomes and WGS (draft)
>> genomes submitted as 500 or fewer contigs. There will be a significant
>> increase in the number
>> of prokaryotic genomes and proteins provided in the RefSeq release.
>>
>> We will avoid providing redundant protein records by providing a
>> single protein record when
>> identical proteins can be annotated on more than one genome.
>>
>> A new RefSeq protein accession prefix, WP_, will be used for these proteins.
>> The accession has the format:
>>
>>  WP_ + 9 numerals + version number, e.g., WP_000000001.1
>>
>> WP_ records will be 'protein-only' records.  When an identical protein
>> is annotated on more
>> than one bacterial genome record, the annotated CDS will point to the
>> same WP_ accession.
>>
>> Thus, a given WP_ record may represent a protein found in more than
>> one strain or in more
>> than one bacterial 'species'.
>>
>> A separate announcement with more details will be provided in the next
>> few weeks.
>>
>> ---
>>
>> This is implemented using the GenBank 'CONTIG' field to point to the
>> actual sequence entry from the various annotation entries. This means
>> that the flat-file data no longer contains the sequence, but NCBI
>> Entrez can construct the sequence when it is requested (e.g. when you
>> ask for fasta), in a similar way to the handling of contig entries in
>> GenBank and RefSeq (nucleotide).
>>
>> All the best,
>>
>> Hamish
>>
>> On 5 June 2013 19:16, Warren Gallin <wgallin at ualberta.ca> wrote:
>>> Hi,
>>>
>>> I am encountering a problem with a number of protein records.
>>>
>>> A HMMer search of the nr database returns a gi number and an associated sequence.
>>>
>>> When I use that gi number to try to retrieve the full GENBANK record, however, there is no sequence returned with the record.
>>>
>>> When I use the NCBI web interface and use that gi number the GENPEPT record returns with no sequence, but when I select fast format the sequence is returned.
>>>
>>> Examples of gi numbers for which this occurs are:
>>>
>>> 23099847
>>> 21224301
>>> 68536697
>>> 46580017
>>> 77359109
>>>
>>> Is this a flaw with the individual GENPEPT records?  In which case should I report it to NCBI?
>>>
>>> Or are these some kind of "special" record that needs different parameters passed on the utilizes search?
>>>
>>> There is a workaround, I guess, where is the sequence comes back empty then a new retrieval of fasta formatted records can be run and the empty field in the GENPEPT record repopulated, but this seems inelegant.
>>>
>>> All advice and/or commentary appreciated.
>>>
>>> Warren Gallin
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>> --
>> ----
>> "Saying the internet has changed dramatically over the last five years
>> is cliché – the internet is always changing dramatically" - Craig
>> Labovitz, Arbor Networks.
>>
>



-- 
----
"Saying the internet has changed dramatically over the last five years
is cliché – the internet is always changing dramatically" - Craig
Labovitz, Arbor Networks.