Find all gene ID from a genome through Entrez

Question

[maxi_zu]

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?

Answer 1

[Pierre Lindenbaum]

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

Answer 2

[5heikki]

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