350
V. Mittard-Runte et al.
Table 9.9 The different ways to retrieve data at GenBank
Sequence retrieval at GenBank
Entrez nucleotide browser
Searches for sequences in Genbank, RefSeq and PDB
dbEST searching
Expressed sequence tags from one of the 6 major organism
groups (Archea, Bacteria, Eukaryota, Viruses, Viroids,
and Plasmids)
dbSTS searching
Sequence tagged sites
dbGSS searching
Genome survey sequences
FTP
Full release and daily updates of GenBank
Genomes
Views provided for genomes from one of the 6 major
organism groups (Archea, Bacteria, Eukaryota, Viruses,
Viroids, and Plasmids)
Table 9.10 Submission tools available at the major public database centres
Direct submissions of DNA sequences
DDBJ (CIB)
EMBL (EBI)
GenBank (NCBI)
Submission tool
Sakura 1
Webin 2
BankIt 3 or Sequin 4
1 http://sakura.ddbj.nig.ac.jp/top-e.html
2 http://www.ebi.ac.uk/embl/Submission/webin.html
3 http://www.ncbi.nlm.nih.gov/BankIt/index.html
4 http://www.ncbi.nlm.nih.gov/Sequin/index.html
(d) Nucleotide Sequence Submissions
How to submit data to one of the nucleotide sequence databases?
If you have one or more sequences to submit (as is often the case for small
laboratories), the direct submission procedures from one of the three sites are recommended (Table 9.10). For long or complex submissions, the database in question
should be contacted in advance for assistance.
If you have many sequences to submit (often the case in large-scale sequencing
centres), each of the three sites offers a bulk submission procedure such as the mass
submission system (MSS) at DDBJ.
For submissions to NCBI of Expressed Sequence Tags (ESTs), Genome Survey
Sequence (GSS), and Sequence Tagged Sites (STS) data, please have a look at the
NCBI website.
For all submissions, it is recommended that the submitter studies the database
website for up to date information on submission at one of the three sites (DDBJ,
EMBL, or GenBank). The databases can be contacted by e-mail at the following
addresses:
DDBJ: ddbjsub@ddbj.nig.ac.jp
EMBL: datasubs@ebi.ac.uk
GenBank: gb-sub@ncbi.nlm.nih.gov
V. Mittard-Runte et al.
Table 9.9 The different ways to retrieve data at GenBank
Sequence retrieval at GenBank
Entrez nucleotide browser
Searches for sequences in Genbank, RefSeq and PDB
dbEST searching
Expressed sequence tags from one of the 6 major organism
groups (Archea, Bacteria, Eukaryota, Viruses, Viroids,
and Plasmids)
dbSTS searching
Sequence tagged sites
dbGSS searching
Genome survey sequences
FTP
Full release and daily updates of GenBank
Genomes
Views provided for genomes from one of the 6 major
organism groups (Archea, Bacteria, Eukaryota, Viruses,
Viroids, and Plasmids)
Table 9.10 Submission tools available at the major public database centres
Direct submissions of DNA sequences
DDBJ (CIB)
EMBL (EBI)
GenBank (NCBI)
Submission tool
Sakura 1
Webin 2
BankIt 3 or Sequin 4
1 http://sakura.ddbj.nig.ac.jp/top-e.html
2 http://www.ebi.ac.uk/embl/Submission/webin.html
3 http://www.ncbi.nlm.nih.gov/BankIt/index.html
4 http://www.ncbi.nlm.nih.gov/Sequin/index.html
(d) Nucleotide Sequence Submissions
How to submit data to one of the nucleotide sequence databases?
If you have one or more sequences to submit (as is often the case for small
laboratories), the direct submission procedures from one of the three sites are recommended (Table 9.10). For long or complex submissions, the database in question
should be contacted in advance for assistance.
If you have many sequences to submit (often the case in large-scale sequencing
centres), each of the three sites offers a bulk submission procedure such as the mass
submission system (MSS) at DDBJ.
For submissions to NCBI of Expressed Sequence Tags (ESTs), Genome Survey
Sequence (GSS), and Sequence Tagged Sites (STS) data, please have a look at the
NCBI website.
For all submissions, it is recommended that the submitter studies the database
website for up to date information on submission at one of the three sites (DDBJ,
EMBL, or GenBank). The databases can be contacted by e-mail at the following
addresses:
DDBJ: ddbjsub@ddbj.nig.ac.jp
EMBL: datasubs@ebi.ac.uk
GenBank: gb-sub@ncbi.nlm.nih.gov