介绍
使用islandpath软件做原核生物基因岛预测。输入gbk文件
输入
gbk文件：
格式例如，
LOCUS NC_003210 2944528 bp DNA circular CON 17-DEC-2014
DEFINITION Listeria monocytogenes EGD-e chromosome, complete genome.
ACCESSION NC_003210
VERSION NC_003210.1 GI:16802048
DBLINK BioProject: PRJNA61583
KEYWORDS RefSeq.
SOURCE Listeria monocytogenes EGD-e
ORGANISM Listeria monocytogenes EGD-e
Bacteria; Firmicutes; Bacilli; Bacillales; Listeriaceae; Listeria.
REFERENCE 1 (bases 1 to 2944528)
AUTHORS Toledo-Arana,A., Dussurget,O., Nikitas,G., Sesto,N.,
Guet-Revillet,H., Balestrino,D., Loh,E., Gripenland,J., Tiensuu,T.,
Vaitkevicius,K., Barthelemy,M., Vergassola,M., Nahori,M.A.,
Soubigou,G., Regnault,B., Coppee,J.Y., Lecuit,M., Johansson,J. and
Cossart,P.
TITLE The Listeria transcriptional landscape from saprophytism to
virulence
JOURNAL Nature 459 (7249), 950-956 (2009)
PUBMED 19448609
REFERENCE 2 (bases 1 to 2944528)
AUTHORS Chatterjee,S.S., Hossain,H., Otten,S., Kuenne,C., Kuchmina,K.,
Machata,S., Domann,E., Chakraborty,T. and Hain,T.
TITLE Intracellular gene expression profile of Listeria monocytogenes
JOURNAL Infect. Immun. 74 (2), 1323-1338 (2006)
PUBMED 16428782
REFERENCE 3 (bases 1 to 2944528)
AUTHORS Glaser,P., Frangeul,L., Buchrieser,C., Amend,A., Baquero,F.,
Berche,P., Bloecker,H., Brandt,P., Chakraborty,T., Charbit,A.,
Chetouani,F., Couve,E., de Daruvar,A., Dehoux,P., Domann,E.,
Dominguez-Bernal,G., Duchaud,E., Durand,L., Dussurget,O.,
Entian,K.-D., Fsihi,H., Garcia-Del Portillo,F., Garrido,P.,
Gautier,L., Goebel,W., Gomez-Lopez,N., Hain,T., Hauf,J.,
Jackson,D., Jones,L.-M., Karst,U., Kreft,J., Kuhn,M., Kunst,F.,
Kurapkat,G., Madueno,E., Maitournam,A., Mata Vicente,J., Ng,E.,
Nordsiek,G., Novella,S., de Pablos,B., Perez-Diaz,J.-C., Remmel,B.,
Rose,M., Rusniok,C., Schlueter,T., Simoes,N., Tierrez,A.,
Vazquez-Boland,J.-A., Voss,H., Wehland,J. and Cossart,P.
TITLE Comparative genomics of Listeria species
JOURNAL Science 294 (5543), 849-852 (2001)
PUBMED 11679669
REFERENCE 4 (bases 1 to 2944528)
CONSRTM NCBI Genome Project
TITLE Direct Submission
JOURNAL Submitted (08-NOV-2001) National Center for Biotechnology
Information, NIH, Bethesda, MD 20894, USA
REFERENCE 5 (bases 1 to 2944528)
AUTHORS Glaser,P., Frangeul,L. and Rusniok,C.
TITLE Direct Submission
JOURNAL Submitted (06-JUN-2001) Glaser P., Institut Pasteur, Genomique des
Microorganismes Pathogenes, 25 rue du Docteur Roux, 75724 Paris
Cedex 15, FRANCE
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from AL591824.
RefSeq Category: Reference Genome
FGS: First Genome sequenced
MOD: Model Organism
UPR: UniProt Genome
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..2944528
/organism="Listeria monocytogenes EGD-e"
/mol_type="genomic DNA"
/strain="EGD-e"
/db_xref="taxon:169963"
regulatory 305..310
/regulatory_class="ribosome_binding_site"
operon 318..3012
/operon="Operon_001"
/experiment="EXISTENCE:[PMID:19448609]"
gene 318..1673
/gene="dnaA"
/locus_tag="lmo0001"
/operon="Operon_001"
/experiment="EXISTENCE:[PMID:19448609]"
/db_xref="GeneID:984365"
CDS 318..1673
/gene="dnaA"
/locus_tag="lmo0001"
/operon="Operon_001"
/experiment="EXISTENCE:[PMID:19448609]"
/note="binds to the dnaA-box as an ATP-bound complex at
the origin of replication during the initiation of
chromosomal replication; can also affect transcription of
multiple genes including itself."
/codon_start=1
/transl_table=11
/product="chromosome replication initiator DnaA"
/protein_id="NP_463534.1"
/db_xref="GI:16802049"
/db_xref="GeneID:984365"
/translation="MQSIEDIWQETLQIVKKNMSKPSYDTWMKSTTAHSLEGNTFIIS
APNNFVRDWLEKSYTQFIANILQEITGRLFDVRFIDGEQEENFEYTVIKPNPALDEDG
IEIGKHMLNPRYVFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHLM
HAVGHYVQQHKDNAKVMYLSSEKFTNEFISSIRDNKTEEFRTKYRNVDVLLIDDIQFL
AGKEGTQEEFFHTFNTLYDEQKQIIISSDRPPKEIPTLEDRLRSRFEWGLITDITPPD
LETRIAILRKKAKADGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLVNKDITA
GLAAEALKDIIPSSKSQVITISGIQEAVGEYFHVRLEDFKAKKRTKSIAFPRQIAMYL
SRELTDASLPKIGDEFGGRDHTTVIHAHEKISQLLKTDQVLKNDLAEIEKNLRKAQNM
F"
''''''
结果
基因岛的位置信息文件
例如
GI_1 351459 374596
GI_2 496381 520791
GI_3 1131558 1161675
