FAQ
Keyword Search
Tag Search(NSSS:DDBJ Nucleotide Sequence Submission System , MSS:Mass Submission System)
We would like to cite the article of DDBJ. analysis searchWhen you kindly describe about using DDBJ on academic papers etc., in general, please use the latest article for DDBJ on Nucleic Acids Res. Database issue as a reference.
However, please note followings.
- In case of citation for each sequence record
- In general, it is enough to describe accession number for it in your publication.
If you discuss about the data in detail, please use primary citation for the data as a reference.
- In case of citation for each service provided at DDBJ
- In general, please use original article for each service as a reference.
Last Updated:June 28, 2017
When you kindly describe about using DDBJ on academic papers etc., in general, please use the latest article for DDBJ on Nucleic Acids Res. Database issue as a reference.
However, please note followings.
- In case of citation for each sequence record
- In general, it is enough to describe accession number for it in your publication.
If you discuss about the data in detail, please use primary citation for the data as a reference. - In case of citation for each service provided at DDBJ
- In general, please use original article for each service as a reference.
Does DDBJ offer data search and analysis services? analysis searchThere are two ways of searching and analyzing data, as discussed below. Please select the option that is appropriate for your needs.
- Conducting searches and analyses using a network server such as an FTP or web server.
You may access these networking tools via Search / Analysis.
- Conducting searches and analyses by logging in to the supercomputer system at the National Institute of Genetics (NIG).
(This requires a supercomputer user ID. You will need to sign up for a new user account on the NIG supercomputer system.)
Last Updated:July 5, 2017
- Conducting searches and analyses using a network server such as an FTP or web server.
You may access these networking tools via Search / Analysis. - Conducting searches and analyses by logging in to the supercomputer system at the National Institute of Genetics (NIG).
(This requires a supercomputer user ID. You will need to sign up for a new user account on the NIG supercomputer system.)
Please distribute clones. analysis PRThe DDBJ is a database center of nucleotide sequences, so it does not distribute any clones.
Please contact the submitter of the clone sequence directly.
Last Updated:February 26, 2016
The DDBJ is a database center of nucleotide sequences, so it does not distribute any clones.
Please contact the submitter of the clone sequence directly.
Is it possible to specify BOOTSTRAP when performing analyses with ClustalW? analysis ClustalWIn ClustalW, BOOTSTRAP calculations are performed for all analyses.
Select [Download Tree File] at the end of the output file to download a .phb file.
Note that .phb files will not be produced if the following combinations of options are chosen for the [FORMAT] and [CLUSTERING] fields of the input form.
[FORMAT] [CLUSTERING]
PHYLIP NJ
NEXUS NJ
PHYLIP UPGMA
NEXUS UPGMA
Last Updated:July 5, 2017
Select [Download Tree File] at the end of the output file to download a .phb file.
Note that .phb files will not be produced if the following combinations of options are chosen for the [FORMAT] and [CLUSTERING] fields of the input form.
| [FORMAT] | [CLUSTERING] |
| PHYLIP | NJ |
| NEXUS | NJ |
| PHYLIP | UPGMA |
| NEXUS | UPGMA |
What are the meanings of the three symbols “*”, “.”, and “:” in ClustalW? analysis ClustalWThese symbols are used to indicate amino acids aligned at the sites marked with the symbol.
“*” indicates perfect alignment.
“:” indicates a site belonging to group exhibiting strong similarity.
“.” indicates a site belonging to a group exhibiting weak similarity.
The criterion for distinguishing strong from weak similarity is as follows: Strong similarity corresponds to a PAM250 MATRIX score between amino acids of greater than 0.5, while weak similarity corresponds to a score of 0.5 or less. In the README excerpt, the lines horizontally adjacent to the phrases
STA
NEQK
:
indicate the amino-acid groups in cases for which the corresponding symbol is present (These are written using single-character notation for amino acids).
The README file included with the ClustalW source package contains the following text.
---------------------------------------------------------------------------
12. The conservation line output in the clustal format alignment file has been changed.
Three characters are now used:
'*' indicates positions which have a single, fully conserved residue
':' indicates that one of the following 'strong' groups is fully conserved:-
STA NEQK
NHQK
NDEQ
QHRK
MILV
MILF
HY
FYW
'.' indicates that one of the following 'weaker' groups is fully conserved:-
CSA
ATV
SAG
STNK
STPA
SGND
SNDEQK
NDEQHK
NEQHRK
FVLIM
HFY
These are all the positively scoring groups that occur in the Gonnet Pam250
matrix. The strong and weak groups are defined as strong score >0.5 and weak
score =<0.5 respectively.
--------------------------------------------------------------------------- Last Updated:June 8, 2015
“*” indicates perfect alignment.
“:” indicates a site belonging to group exhibiting strong similarity.
“.” indicates a site belonging to a group exhibiting weak similarity.
The criterion for distinguishing strong from weak similarity is as follows: Strong similarity corresponds to a PAM250 MATRIX score between amino acids of greater than 0.5, while weak similarity corresponds to a score of 0.5 or less. In the README excerpt, the lines horizontally adjacent to the phrases
STA
NEQK
:
indicate the amino-acid groups in cases for which the corresponding symbol is present (These are written using single-character notation for amino acids).
The README file included with the ClustalW source package contains the following text.
---------------------------------------------------------------------------
12. The conservation line output in the clustal format alignment file has been changed.
Three characters are now used:
'*' indicates positions which have a single, fully conserved residue
':' indicates that one of the following 'strong' groups is fully conserved:-
STA NEQK
NHQK
NDEQ
QHRK
MILV
MILF
HY
FYW
'.' indicates that one of the following 'weaker' groups is fully conserved:-
CSA
ATV
SAG
STNK
STPA
SGND
SNDEQK
NDEQHK
NEQHRK
FVLIM
HFY
These are all the positively scoring groups that occur in the Gonnet Pam250
matrix. The strong and weak groups are defined as strong score >0.5 and weak
score =<0.5 respectively.
---------------------------------------------------------------------------
We would like to acknowledge the NIG Supercomputer System in our publication. analysis format searchThe activity of the NIG Supercomputer System are evaluated by the acknowledgments of all of you.
Please acknowledge in your papers, presentations and other publications, the role of NIG Supercomputer System played in your research.
It is no problem to modify the following example for the connection of sentences.
Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.
Last Updated:June 26, 2017
The activity of the NIG Supercomputer System are evaluated by the acknowledgments of all of you.
Please acknowledge in your papers, presentations and other publications, the role of NIG Supercomputer System played in your research.
It is no problem to modify the following example for the connection of sentences.
Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.
We would like to acknowledge DDBJ in our publication. analysis format searchWhen you use DDBJ services in your research, we would appreciate it if you would include a reference to DDBJ in your publications.
If you consider citation of DDBJ paper is unsuitable, please consider to acknowledge in your publications, the role of DDBJ services played in your research.
It is no problem to modify the following example for the connection of sentences.
This research was performed using "name of DDBJ Service, analytical tools".
Last Updated:June 26, 2017
When you use DDBJ services in your research, we would appreciate it if you would include a reference to DDBJ in your publications.
If you consider citation of DDBJ paper is unsuitable, please consider to acknowledge in your publications, the role of DDBJ services played in your research.
It is no problem to modify the following example for the connection of sentences.
This research was performed using "name of DDBJ Service, analytical tools".
