User: heath
heath • 20
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Posts by heath
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... No problem...I have solved this question. thx!
...
written 6.0 years ago by
heath • 20
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... Hey all,
if I have a protein gi? is there a fast way to find its nearest global structure/sequence neighbor and retrieve top 10/20 hits as protein gi's along with e-value and sequence/structure identities etc? can blastp command line obtain these?
Thanks!
...
written 6.0 years ago by
heath • 20
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Comment:
C: Ncbi Entrez Server Issues
... Thanks a lot :-) !!
...
written 7.2 years ago by
heath • 20
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... Dear All,
I am using entrez protein data base for searching a list 40 000 of protein ids, I set stop time (0.3) to keep ncbi server happy
my program runs OK at first, but after running 1hrs or so..it shows
File "snpinfo_new.py", line 31, in <module>
fg=Entrez.efetch(db='protein', id=uid, ...
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... Thanks a lot for replying and sorry for confusing.. It does not really matter the retmode/rettype is 'xml' or'gb' ..I think at the moment I should simplify the question into "how i use Refseq id of a protein to obtain its Gi and CDD information."
...
written 7.2 years ago by
heath • 20
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... eh...i am not sure if.Biopython is able to pass the xml from db='protein'. biopython should be able to parse most of the xml from entrez but not each one as long as I know... i can somehow put the above information into SeqIO.read(), and convert it into the Bio.SeqRecord but i can only have followi ...
written 7.3 years ago by
heath • 20
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... if the rettype change to "gb"
handle= Entrez.efetch(db='protein', id='NP_000368.1', rettype='gb')
In [26]: ret=SeqIO.read(handle,'genbank')
In [27]: feats=set()
In [28]: for feat in ret.features:
....: feats.add(feat.type)
....:
In [29]: feats
Out[29]: set(['source', 'Protein', 'CDS' ...
written 7.3 years ago by
heath • 20
• updated
7.3 years ago by
Istvan Albert ♦♦ 84k
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... I want to obtain a proteins gi no# along with its cd root no# and taxid from a proteins NP_xxx. 1 (id#)
when I use the Biopython's entrez as following
handle= Entrez.efetch(db='protein', id='NP_000368.1', retmode='xml')
record= Entrez.read(handle)
the record is a list-elements object.and look ...
written 7.3 years ago by
heath • 20
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... Thanks a lot :-) .!
...
written 7.3 years ago by
heath • 20
2
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... Hey all,
I have issues on the output of rsid from dbSNP, if i use the website base output for specific terms of the protein I got an list of rsid no# around 13000,
http://www.ncbi.nlm.nih.gov/snp/details?querykey=3
(pathogenic[Clinical_Significance] OR probable pathogenic[Clinical_Significance]) ...
Latest awards to heath
Popular Question
5.6 years ago,
created a question with more than 1,000 views.
For How I Get The Fasta Sequences Of Proteins From A List Of Protien Pdb Id
Popular Question
5.6 years ago,
created a question with more than 1,000 views.
For Ncbi Entrez Server Issues
Popular Question
5.6 years ago,
created a question with more than 1,000 views.
For How To Parse The Xml From Entrez Db=Protein Using Biopython
Popular Question
5.6 years ago,
created a question with more than 1,000 views.
For Query Returns A Different Number Of Results When Fetching With Biopython From Dbsnp
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5.6 years ago,
created a question with more than 1,000 views.
For Issues In Parsing The Xml For Dbsnp Via Biopython
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