Question: Find all gene ID from a genome through Entrez
0
gravatar for maxi_zu
5.7 years ago by
maxi_zu0
France
maxi_zu0 wrote:

Hey,

I want to find all the gene of a specific genome through a genome number accession.

I need to fin all the Gene ID

I try to deal with Entrez and BioPython, so I first do that :

from Bio import Entrez
handle = Entrez.esearch(db="nuccore",term="NC_003210")
record = Entrez.read(handle)
print record
{u'Count': '1', u'RetMax': '1', u'IdList': ['16802048'], u'TranslationSet': [], u'RetStart': '0', u'QueryTranslation': ''}

 

I only have one IdList, and I don't find a way to have all the gene id from this genome.

Someone could help me please ?

 

 

entrez ncbi gene • 2.1k views
ADD COMMENTlink modified 5.7 years ago by 5heikki9.0k • written 5.7 years ago by maxi_zu0
1
gravatar for Pierre Lindenbaum
5.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

NC_003210 is  Listeria monocytogenes EGD-e . Taxon-ID=169963 =

http://www.ncbi.nlm.nih.gov/gene/?term=txid169963[Organism:noexp]

so the esearch cmd line to gene the gene-ids  would be something like:

 (curl 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=txid169963%5BOrganism:noexp%5D&retmax=5000' | xmllint --xpath "translate(normalize-space(//IdList),' ',',')" - && echo) | tr "," "\n"

(...)

984470
984464
984454
984452
984451
984449
984448
984443
984438
984407
984406
984405
984398
984395
984394
984391
984382
984380
984366

 

ADD COMMENTlink written 5.7 years ago by Pierre Lindenbaum130k
0
gravatar for 5heikki
5.7 years ago by
5heikki9.0k
Finland
5heikki9.0k wrote:

First few lines with entrez direct:

esearch -db nuccore -query NC_003210 | elink -target gene | efetch -format id


1. inlA

internalin A[Listeria monocytogenes EGD-e]

Other Aliases: lmo0433

Annotation: NC_003210.1 (454534..456936)

ID: 985151


2. inlB

internalin B[Listeria monocytogenes EGD-e]

Other Aliases: lmo0434

Annotation: NC_003210.1 (457021..458913)

ID: 986892


3. prfA

peptide chain release factor 1[Listeria monocytogenes EGD-e]

Other Aliases: lmo2543

Annotation: NC_003210.1 (2619415..2620491, complement)

ID: 986736


4. hly

listeriolysin O precursor[Listeria monocytogenes EGD-e]

Other Aliases: lmo0202

Annotation: NC_003210.1 (205819..207408)

ID: 987033


5. sigB

RNA polymerase sigma factor SigB[Listeria monocytogenes EGD-e]

Other Aliases: lmo0895

Annotation: NC_003210.1 (930671..931450)

ID: 986527


6. prfA

listeriolysin positive regulatory protein[Listeria monocytogenes EGD-e]

Other Aliases: lmo0200

Annotation: NC_003210.1 (203640..204353, complement)

ID: 987031


7. actA

actin-assembly inducing protein precursor[Listeria monocytogenes EGD-e]

Other Aliases: lmo0204

Annotation: NC_003210.1 (209470..211389)

ID: 987035


8. fri

non-heme iron-binding ferritin[Listeria monocytogenes EGD-e]

Other Aliases: lmo0943

Annotation: NC_003210.1 (979059..979529)

ID: 986847


9. iap

invasion associated secreted endopeptidase[Listeria monocytogenes EGD-e]

Other Aliases: lmo0582

Annotation: NC_003210.1 (618932..620380, complement)

ID: 985140


10. inlC

internalin C[Listeria monocytogenes EGD-e]

Other Aliases: lmo1786

Annotation: NC_003210.1 (1860200..1861090, complement)

ID: 985945


11. plcA

phosphatidylinositol-specific phospholipase c[Listeria monocytogenes EGD-e]

Other Aliases: lmo0201

Annotation: NC_003210.1 (204624..205577, complement)

ID: 987032
ADD COMMENTlink written 5.7 years ago by 5heikki9.0k
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