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[求助]
如何处理基因注释文件
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我现在下载了GI编号为NC_000853的基因注释信息，在注释信息里卖弄有很多是可以编码蛋白质的基因，我现在想把这些基因提取出来，如果一个一个地提取效率太低，想问下大家有什么比较高效的方法吗？？ 下面的红线加粗的字体就是可以编码蛋白质的基因所在序列的位置，这种片段特别多，不知道怎么编程可以快速地获取该genome中所有的gene ,求大神哈！！ LOCUS NC_000853 1860725 bp DNA circular CON 22-DEC-2014 DEFINITION Thermotoga maritima MSB8 chromosome, complete genome. ACCESSION NC_000853 VERSION NC_000853.1 GI:15642775 DBLINK BioProject: PRJNA57723 KEYWORDS RefSeq. SOURCE Thermotoga maritima MSB8 ORGANISM Thermotoga maritima MSB8 Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga. REFERENCE 1 (bases 1 to 1860725) AUTHORS Nelson,K.E., Clayton,R.A., Gill,S.R., Gwinn,M.L., Dodson,R.J., Haft,D.H., Hickey,E.K., Peterson,J.D., Nelson,W.C., Ketchum,K.A., McDonald,L., Utterback,T.R., Malek,J.A., Linher,K.D., Garrett,M.M., Stewart,A.M., Cotton,M.D., Pratt,M.S., Phillips,C.A., Richardson,D., Heidelberg,J., Sutton,G.G., Fleischmann,R.D., White,O., Salzberg,S.L., Smith,H.O., Venter,J.C. and Fraser,C.M. TITLE Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima JOURNAL Nature 399 (6734), 323-329 (1999) PUBMED 10360571 REFERENCE 2 (bases 1 to 1860725) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (18-SEP-2001) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 3 (bases 1 to 1860725) AUTHORS Nelson,K.E., Clayton,R.A., Gill,S.R., Gwinn,M.L., Dodson,R.J., Haft,D.H., Hickey,E.K., Peterson,J.D., Nelson,W.C., Ketchum,K.A., McDonald,L., Utterback,T.R., Malek,J.A., Linher,K.D., Garrett,M.M., Stewart,A.M., Cotton,M.D., Pratt,M.S., Phillips,C.A., Richardson,D., Heidelberg,J., Sutton,G.G., Fleischmann,R.D., White,O., Salzberg,S.L., Smith,H.O., Venter,J.C. and Fraser,C.M. TITLE Direct Submission JOURNAL Submitted (01-JUN-1999) The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from AE000512. RefSeq Category: Reference Genome TYS: Designated Type Strain UPR: UniProt Genome COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..1860725 /organism="Thermotoga maritima MSB8" /mol_type="genomic DNA" /strain="MSB8" /db_xref="taxon:243274" gene 323..448 /locus_tag="TM0001" /db_xref="GeneID:897248" CDS 323..448 /locus_tag="TM0001" /note="similar to percent identity: 0.00; identified by sequence similarity" /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="NP_227817.1" /db_xref="GI:15642776" /db_xref="GeneID:897248" /translation="MVYGKEGYGRSKNILLSECVCGIISLELNGFQYFLRGMETL" gene complement(483..608) /locus_tag="TM0002" /db_xref="GeneID:896810" CDS complement(483..608) /locus_tag="TM0002" /note="similar to percent identity: 0.00; identified by sequence similarity" /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="NP_227818.1" /db_xref="GI:15642777" /db_xref="GeneID:896810" |
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2楼2016-03-07 23:05:34
江天一览3215
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