次世代シーケンサーデータの解析手法 第9回 ゲノムアノテー …

1 9 DDBJ Vol. 28 No. 1 3 11 2017 9 3 2,400,619 bytes 8 W28 1-2 Bio-Linux 3 1 8 wget 4 ~/Desktop/mac_share W1-1 DNA 4 A T C G %A %T %C %G DNA 2 Chargaff s second parity rule 5 W1-2 DNA origin of replication oriC C G

2 6-11 GC skew G C / G C 7 oriC 9 DDBJ 1 2 1 2 1* 3 3*1 2 DDBJ 3 International Nucleotide Sequence Database Collaboration; INSDC 9 Lactobacillus hokkaidonensis LOOC260T INSDC DNA Data Bank of Japan DDBJ DNAP lotter R URL: ~ URL: ~ #about_book_JSLAB W Key words replication origin, annotation, INSDC, DDBJ To whom correspondence should be addressed.

3 Phone +81-3-5841-2395 Fax +81-3-5841-1136 E-mail or 3 Japanese Journal of Lactic Acid BacteriaCopyright 2017, Japan Society for Lactic Acid Bacteria oriC DnaA DnaA box DnaA oriC 12-14 GC skew C G / G C 6 11 dnaA DFAST 15 sequence1 dnaA W2-1 DFAST chromosome 1436009, 1437325 bp dnaA W2-2 oriC dnaA 1.

4 437,325 Ori-Finder 16 oriC W3-1 Ori-Finder GC skew 1 Z-curve 17 DnaA box dnaA Ori-Finder 1 single-FASTA multi-FASTA 1 2 single-FASTA W3-2 Ori-Finder W3-3 Ori-Finder 3 oriC W3-4 1396338, 1396990 bp 1435834, 1436008 bp 1437326, 1438021 bp 3 oriC 1,437,326 DFAST dnaA 1,437,325 1,437,325 dnaA ATG GTG W4-1 GTG TTG W4-2 L.

5 Hokkaidonensis ATG W4-3 dnaA 1,437,325 100 1,437,425 dnaA 1, 1437425 bp 1437426, 2277983 bp W4-4 Python W4-5 Linux EMBOSS 18 revseq W4-8 19 20 coding sequence CDS tRNA rRNA BLAST Pfam Rfam DB

6 21 INSDC DDBJ 21 GenBank 22 ENA 23 INSDC DB ENA EMBL European Molecular Biology Laboratory DB EMBL DDBJ 4 Vol. 28, No. 1 Japanese Journal of Lactic Acid Bacteria DDBJ DB DDBJ ENA DB EMBL EBI The European Bioinformatics Institute GenBank DB NCBI National Center for Biotechnology Information DB NCBI GenBank EMBL-EBI ENA 3 24 25 INSDC DDBJ NCBI EMBL-EBI DDBJ SRA DRA EMBL-EBI ENA ENA NCBI SRA SRA DB INSDC 1

7 DB INSDC INSDC INSDC entry feature qualifier 3 GenBank GenBank DDBJ GenBank DDBJ ENA ENA EMBL INSDC EMBOSS 18 seqret 1 26 BioPerl 27 Biopython 28 BioRuby 29 entry 1 entry 1 1 entry 1 entry entry feature feature location feature qualifier DDBJ entry K-12 1 U00096 entry 3 W5-1 2 1 2 W5-2 U00096 K-12

8 Entry 18 REFERENCE 1 1997 30 entry feature W5-3 source feature feature entry 1 W5-4 gene feature CDS rRNA tRNA CDS feature W5-5 1 1 gene feature 1 gene feature CDS feature CDS feature qualifier gene qualifier product qualifier translation qualifier W5-6 experiment qualifier W5-7 gene CDS feature tRNA feature rRNA feature repeat_region feature W5-8 ncRNA feature W5-9 qualifier feature INSDC Feature Table Definition W5-10 feature feature qualifier DDBJ W5-11 locus_tag locus_tag qualifier

9 W6-1 K-12 U00096 locus_tag qualifier locus_tag W6-2 3 5 Jpn. J. Lactic Acid Bact. Vol. 28, No. 1 1 DDBJ K-12 gene feature* CDS rRNA tRNA 1 gene feature CDS feature 6 Vol. 28, No. 1 Japanese Journal of Lactic Acid Bacteria locus_tag prefix tag prefix_tag 2014 L. hokkaidonensis 1 GenBank accession AP014680 1 feature locus_tag LOOC260_100010 W6-3 prefix INSDC locus_tag prefix AP014680 LOOC260 locus_tag prefix tag 10 W6-4 tRNA t0001 rRNA r0001 gene feature CDS feature locus_tag locus_tag

10 W6-5 DDBJ ENA gene feature 2 gene feature GenBank GenBank gene feature