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Find open reading frames

This function will find open reading frames greater than an specified length. The results can be output in two ways, either in feature table format


FT   CDS             120..233
FT   CDS             161..256
FT   CDS             301..396
FT   CDS             333..497
FT   CDS             512..736
FT   CDS             525..965
FT   CDS             740..952
FT   CDS             754..876
FT   CDS             956..1789

or as a fasta file.

>120                 120..233
VISENISLLKIGAKNHHWLLKQLLKMSMGGFCCVNVIY*
>161                 161..256
EPSLAVKTVIKNVNGWFLLCKCHLLNRYLFLD*
>301                 301..396
ICCARTCAICDLKHALSPVFTRYLQFFMIEQG*
>333                 333..497
SEARFITSVYALFTVFHDRTGLAEKSQLYALEKYLNIYSPFGYLLFEITGAHRII*
>512                 512..736
CLTLSLKESFIRHAAYLEGSRSEKRDVCVARESKRCSEASARSVTGGDSKWIAVQPQRPL
LGRLCNKRGPGSLSA*
>525                 525..965
ALKKVLYDTRHTSKGAGVKNVMSVSLVSRNVARKLLLVQLLVVIASGLLFSLKDPFWGVS
AISGGLAVFLPNVLFMIFAWRHQAHTPAKGRVAWTFAFGEAFKVLAMLVLLVVALAVLKA
VFLPLIVTWVLVLVVQILAPAVINNKG*
>740                 740..952
RFVYDICLASPGAYTSERPGGLDIRIWRSFQSSGDVGVTGGGVGGFKGGILAADRYVGFG
AGGSDTGTGCN*
>754                 754..876
YLPGVTRRIHQRKAGWPGHSHLAKLSKFWRCWCYWWWRWRF*
>956                 956..1789
QQRVKGIMASENMTPQDYIGHHLNNLQLDLRTFSLVDPQNPPATFWTINIDSMFFSVVLG
LLFLVLFRSVAKKATSGVPGKFQTAIELVIGFVNGSVKDMYHGKSKLIAPLALTIFVWVF
LMNLMDLLPIDLLPYIAEHVLGLPALRVVPSADVNVTLSMALGVFILILFYSIKMKGIGG
FTKELTLQPFNHWAFIPVNLILEGVSLLSKPVSLGLRLFGNMYAGELIFILIAGLLPWWS
QWILNVPWAIFHILIITLQAFIFMVLTIVYLSMASEEH*

The user can select that start and end points over which to do the search, which strand to search (either the forward, reverse or both) and the minimum length of the open reading frame in codons. If the output is being written in fasta format, the name of file is also required.

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/nip4_14.html