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Old 03-18-2014, 10:46 PM   #1
vivienne_lovely
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Default how to convert gff and fasta file to genbank format

Hi everyone,
I want convert gff and fasta file to genbank format, is there a software or perl
script can do this? Waiting for your help. Thank you.
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Old 03-19-2014, 06:09 AM   #2
TiborNagy
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Maybe this thread can help:
http://seqanswers.com/forums/showthread.php?t=40652
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Old 03-19-2014, 07:40 PM   #3
vivienne_lovely
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Hi TiborNagy,
Thank you for your reply. I already tried that before,but that is not just what I wanted. That tool can convert gff or fasta to genbank format, but it can not convert gff and fasta to genbank like follows which contains both annotation and sequence.

LOCUS OB_HTE831 3630528 bp DNA circular BCT 11-DEC-2002
DEFINITION Oceanobacillus iheyensis HTE831, complete genome.
ACCESSION
VERSION
KEYWORDS .
SOURCE Oceanobacillus iheyensis HTE831
ORGANISM Oceanobacillus iheyensis HTE831
Bacteria; Firmicutes; Bacillales; Oceanobacillus.
REFERENCE 1 (bases 1 to 3630528)
AUTHORS Takami,H., Takaki,Y. and Uchiyama,I.
TITLE Genome sequence of Oceanobacillus iheyensis isolated from the Iheya
Ridge and its unexpected adaptive capabilities to extreme
environments
JOURNAL Nucleic Acids Res. 30 (18), 3927-3935 (2002)
PUBMED 12235376
REFERENCE 2 (bases 1 to 3630528)
AUTHORS Takami,H., Takaki,Y. and Chee,G.
TITLE Direct Submission
JOURNAL Submitted (26-DEC-2001) Hideto Takami, Japan Marine Science and
Technology Center, Deep-sea Microorganisms Research Group; 2-15
Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
FEATURES Location/Qualifiers
source 1..3630528
/organism="Oceanobacillus iheyensis HTE831"
/strain="HTE831"
/db_xref="taxon:221109"
gene 1830..2966
/gene="dnaN"
/locus_tag="OBB_0002"
CDS 1830..2966
/gene="dnaN"
/locus_tag="OBB_0002"
/EC_number="2.7.7.7"
/codon_start=1
/transl_table=11
/product="DNA-directed DNA polymerase III beta chain"
/translation="MRFTIQRDKLINGVSNVMKAISARTVIPILTGMKIEVKNHGVTL
TGSDSDISIEYYIPIEEDGIVHVENIEEGTIILQAKYFPDIVRKLPESTVDIVVDDQL
NVRITSGKAEFNLNGQSAEEYPQLPKVQTENSFELPIDLLKSMIKQTVFAVSTMETRP
ILTGVNLKLVDNSLSFTATDSHRLARREIPVSNAPIEISQIVVPGKSLNELNKILGDS
EETVEISVTNNQILFRTKHLNFLSRLLDGNYPETSRLIPEQSKTKIQLKTKELLGTID
RASLLAKEERNNVVKFNAPGNSMIEISSNSPEVGNVVEEITADQMEGEDVKISFSSKY
MIDALKAIEYDEVQIEFTGAMRPFIIRPVGDDSILQLILPVRTY"
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Old 03-20-2014, 05:43 AM   #4
TiborNagy
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You can use seqret from emboss.
Source
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Old 03-20-2014, 05:23 PM   #5
vivienne_lovely
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Thank you. I will try it.
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