插入序列（IS）是原核基因组中最小但最丰富的可移动元件 ISEScan用于原核生物基因组中的IS元件的鉴定

基因组序列： fasta格式，例如 >tig00000462_pilon_pilon CCAGCACCGGGTGGCCGTTGCGCCGCGCGTCCGACAGCCGCTCCAGCAGCAGCATGCCCACACCCTCGCCCCAGCCCGTG CCGTCCGCGGCGGCCGCGAACGCCTTGCACCGGCCGTCCGGCGCGAGACCCCGCTGACGGCTGAACTCCACGAAGAGGCC GGGCGTGGACATCACGGTCACGCCACCGGCGAGGGCGAGCGGGCACTCCCCCTGCCGCAGGGACTGCACCGCGAGATGCA GTGCCACCAGCGACGACGAGCAGGCGGTGTCCACCGTCACCGCGGGCCCCTCGAAGCCGAAGGTGTAGGAGAGCCGACCC GACATGACGCTGGCCGCGCCGCTGGT...

结果表格文件 例如 >tig00000462_pilon_pilon 1 38904 - 2 1.213472 I:942,38813, D: 38989 40625 - 1 1.194179 I: D:40057, 40644 40814 + 3 1.324823 I: D: 40848 41092 + 3 1.372382 I: D:41080, 41221 42474 - 1 1.216103 I: D: 42729 45808 + 3 1.183207 I: D:44266,

使用islandpath软件做原核生物基因岛预测。输入gbk文件

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" ''''''

基因岛的位置信息文件 例如 GI_1 351459 374596 GI_2 496381 520791 GI_3 1131558 1161675

使用phispy软件，对基因组序列做前噬菌体预测

gbk文件 例如 LOCUS ntrd02_1 4133097 bp DNA circular BCT 06-MAR-2006 DEFINITION Roseobacter denitrificans. 4133097 bp, complete sequence. ACCESSION NC_008209 VERSION NC_008209.0 KEYWORDS HTG. SOURCE Roseobacter denitrificans ORGANISM Roseobacter denitrificans Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Roseobacter. REFERENCE 1 (bases 1 to 4133097) (base) [root@localhost g_eggnog_mapper_120749_732415]# less /home/bioinfor/software/cgview/cgview_xml_builder/sample_input/R_denitrificans.gbk (base) [root@localhost g_eggnog_mapper_120749_732415]# head -n 100 /home/bioinfor/software/cgview/cgview_xml_builder/sample_input/R_denitrificans.gbk LOCUS ntrd02_1 4133097 bp DNA circular BCT 06-MAR-2006 DEFINITION Roseobacter denitrificans. 4133097 bp, complete sequence. ACCESSION NC_008209 VERSION NC_008209.0 KEYWORDS HTG. SOURCE Roseobacter denitrificans ORGANISM Roseobacter denitrificans Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Roseobacter. REFERENCE 1 (bases 1 to 4133097) AUTHORS Swingley,W.D., Gholba,S., Mastrian,S.D., Matthies,H.J., Hao,J., Ramos,H., Acharya,C.R., Conrad,A.L., Taylor,H.L., Dejesa,L.C., Shah,M.K., O'Huallachain,M.E., Lince,M.T., Blankenship,R.E., Beatty,J.T. and Touchman,J.W. TITLE A ubiquitous marine phototroph with a novel carbon-fixation pathway JOURNAL Unpublished REFERENCE 2 (bases 1 to 4133097) AUTHORS Touchman,J.W. TITLE Direct Submission JOURNAL Submitted (01-MAR-2006) Pathogen Genomics Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, Arizona 85004, USA FEATURES Location/Qualifiers source 1..4133097 /organism="Roseobacter denitrificans" /mol_type="genomic DNA" /strain="OCh 114" /db_xref="taxon:2434" /chromosome="Chromosome" gene 1723..2871 /locus_tag="RD0003" CDS 1723..2871 /locus_tag="RD0004" /EC_number="2.1.2.10" /note="no close characterized matches identified by match to protein family HMM PF01571" /codon_start=1 /transl_table=11 /product="aminomethyltransferase, putative" /translation="MAIIYRTSALAQRHAEIGGELEDWNGMGTAWFYDHSDERAKADY EAVRTKAGLMDVSGLKKIHLSGPHAAAVIDRATTRNVDKLMPGRAVYAAMLDDRGLFI DDCVIYRLSVNNWLLVHGTGTGHESLAMAAYGKNVSMIFDDDLHDMSLQGPVAVDFLA KHVPGIRDLAYFGIIQTKLFGMPVMISRTGYTGERGYEIFCEGRHAIALWDAILEDGK DMGIRPVQFSTLDLLRTESYLLFYPGDNSETYPFENGAACGDSLWELGLEFTVSPGKT GFRGAENHYALEGKERFKIYGVRLEGTTAADEGADLLKDGEKVGVVTYGMRSDLFDHT VGIARMPVECATPGTKMTVRNGDGTEIPCVAEEMPFYDKDKAIRTAKG" ......

结果表格文件 prophage_coordinates.tsv 例如 pp1 NC_002737 529631 569288 529591 529606 570494 570509 CATGTACAACTATAC CATGTACAACTATAC Longest Repeat flanking phage and within 2000 bp pp2 NC_002737 778642 820599 778526 778576 820960 821010 AAACTCAAGAAGTGATTAAATAAAACATTAAAGAACCTTGTCATATCAAC AAACTCAAGAAGTGATTAAATAAAACATTAAAGAACCTTGTCATATCAAC Longest Repeat flanking phage and within 2000 bp pp3 NC_002737 1191309 1222549 1193572 1193583 1220349 1220360 TCAGATTTTTT AAAAAATCTGA Longest Repeat flanking phage and within 2000 bp pp4 NC_002737 1775862 1785658 1774377 1774389 1782817 1782829 AAATGACTAAGT ACTTAGTCATTT Longest Repeat flanking phage and within 2000 bp

使用minCED软件做CRISPRs分析。可用于基因组或宏基因组数据。

基因组序列： 例如， >tig00000462_pilon_pilon CCAGCACCGGGTGGCCGTTGCGCCGCGCGTCCGACAGCCGCTCCAGCAGCAGCATGCCCACACCCTCGCCCCAGCCCGTG CCGTCCGCGGCGGCCGCGAACGCCTTGCACCGGCCGTCCGGCGCGAGACCCCGCTGACGGCTGAACTCCACGAAGAGGCC GGGCGTGGACATCACGGTCACGCCACCGGCGAG...

结果文件示例 Sequence 'tig00000462_pilon_pilon' (8900851 bp) CRISPR 1 Range: 79635 - 79720 POSITION REPEAT SPACER -------- ----------------------- ---------------------------------------- 79635 CTTCGCCCTCGCCGTGGCCGCCT TCGCCCTCACCCTGGCGGCCTTCGCCCTCACCCCGGCCGC [ 23, 40 ] 79698 CTTCGCCCTCGCCGTGGCCGCCT -------- ----------------------- ---------------------------------------- Repeats: 2 Average Length: 23 Average Length: 40 CRISPR 2 Range: 471329 - 471425 POSITION REPEAT SPACER -------- ---------------------------------- ----------------------------- 471329 CGCTGACGCCGGTATCGGTGCCGCTGACGCCGGT ATCGGTGCCGCTGACGCCGGTATCGGTGC [ 34, 29 ] 471392 CGCTGACGCCGGTATCGGTGCCGCTGACGCCGGT -------- ---------------------------------- ----------------------------- Repeats: 2 Average Length: 34 Average Length: 29