24小时热门版块排行榜

返回列表

初出茅庐521

铜虫 (小有名气)

应助: 0 (幼儿园)
金币: 595.1
散金: 25
红花: 1
沙发: 1
帖子: 81
在线: 25.7小时
虫号: 3986027
注册: 2015-07-23
性别: GG
专业: 微生物资源与分类学

[求助] 如何处理基因注释文件

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"

回复此楼