Dear,
I have an embl file containing these lines
FT CDS complement(2232788..2233492)
FT /systematic_id="SARLGA251_20000"
when I use
extractfeat -sequence embl::LGA251_reduced.embl -type CDS
on emboss version 6.1, the output contains these lines for the
corresponding CDS:
>SARLGA251_2232788_2233492 [CDS]
t
and on emboss version 6.0, the output contains these lines:
>SARLGA251_2232788_2233492 [CDS]
atggctagtgttttatatcaacatggtacattaggcacattaatggcaggtttattaaaa
ggaactgcatcaataaatgaattattgcaacatggtgatttaggtatcgctacactaaca
ggttcaaatggtgaggtcatctttttagatggaaaagcctatcatgcaaatgaacataaa
gaatttgtggaattaaaaggtgatgagttaacaccatatgcaactgtaactaaatttgta
gcagatacaagctatgaaacgaaagataaatcttctgaagcagtttttgcagaaattaag
gaaaagatgttgagtgaaaatttattttctgcagtaaaaatttcaggtgtgtttaaaaaa
atgcatgtacgtatgatgccggcacaagagccaccttatacacgtttaattgattcagct
agaagacaacctgaacaaactgaaacatacgtcaaaggttcagtcgttgggttctttaca
ccagaactattccatggtatcgggtcagcaggattccatgtacactttgcaaatgatgat
cgtaactttggtggacatgtcttagattttgaagtagaagatgttaaggtagaaatccaa
aatatagaaacatttgaacagcattttccaattcaagatgaagatttcataaatgcaaat
attgactataaagatattgcagacgaaattagagaagctgaataa
Does anyone know why it is not extracting the correct sequence for the
CDS features with the latest version of emboss? I am running it on Mac
OSX and I've installed it with fink.
Thanks in advance for your help.
Kind regards,
Anne.
--
Dr Anne Pajon - Pathogen Genomics
Sanger Institute, Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SA, United Kingdom
+44 (0)1223 494 798 (office) | +44 (0)7958 511 353 (mobile)
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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