User: heath

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heath20
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20
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New User
Location:
United States
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3 years, 9 months ago
Joined:
7 years, 4 months ago
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Posts by heath

<prev • 18 results • page 1 of 2 • next >
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Answer: A: how to find proteins nearest neighbors
... No problem...I have solved this question. thx! ...
written 6.0 years ago by heath20
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how to find proteins nearest neighbors
... 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!   ...
sequence alignment blast written 6.0 years ago by heath20
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Comment: C: Ncbi Entrez Server Issues
... Thanks a lot :-) !! ...
written 7.2 years ago by heath20
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Ncbi Entrez Server Issues
... 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, ...
ncbi protein dbsnp biopython entrez written 7.2 years ago by heath20 • updated 6.4 years ago by Peter5.8k
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Comment: C: How To Parse The Xml From Entrez Db=Protein Using Biopython
... 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 heath20
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Comment: C: How To Parse The Xml From Entrez Db=Protein Using Biopython
... 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 heath20
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Comment: C: How To Parse The Xml From Entrez Db=Protein Using Biopython
... 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 heath20 • updated 7.3 years ago by Istvan Albert ♦♦ 84k
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(Closed) How To Parse The Xml From Entrez Db=Protein Using Biopython
... 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 ...
xml protein biopython entrez written 7.3 years ago by heath20
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Comment: C: Query Returns A Different Number Of Results When Fetching With Biopython From Db
... Thanks a lot :-) .! ...
written 7.3 years ago by heath20
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Query Returns A Different Number Of Results When Fetching With Biopython From Dbsnp
... 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]) ...
dbsnp biopython entrez written 7.3 years ago by heath20 • updated 5.2 years ago by Biostar ♦♦ 20

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
Popular Question 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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