Last updated:2015.6.3.

FAQ

Keyword Search

Tag Search(NSSS:DDBJ Nucleotide Sequence Submission System , MSS:Mass Submission System)

FAQs 9 : Tag = blast
I did not obtain the search results that I was expecting. Did I make a mistake in conducting my search? ARSA BLAST getentry search
The DDBJ/EMBL/GenBank data banks share the sequences stored within each data bank, and in principle all three data banks should contain the same data. However, due to time delays in the inter-data-bank sharing of data released by individual data banks, as well as delays between the time at which data are entered into a data bank and the time at which the data are reflected in the corresponding search service, searches conducted using different services at the similar time on the same day may yield slightly different results. If you do not obtain the search results that you were expecting, time delays of this sort are the most likely culprit; however, for cases requiring a more detailed investigation, please contact the DDBJ via the “Other general questions” section of the contact portal. In this case, make sure to specify the following information:
  • The name of the search program and/or the URL that you used to conduct the search.
  • The search conditions that you used.
  • The date and time at which you conducted the search.
  • Accession number of the entry that should have been found.
  • URL of the search results.
  • Any other relevant information.
Also, please see the sections of this document corresponding to the following questions.
Last Updated:June 8, 2015
Where can I find the original papers and other related papers on the DDBJ search and analysis software? BLAST ClustalW search
Please see the DDBJ home page How to Use DDBJ Reference.
Last Updated:April 13, 2016
Is it possible to view search results at a later time? BLAST search
Search results may be accessed via the following URL, which contains a Request ID field.
http://blast.ddbj.nig.ac.jp/blast/r/Request ID
Request ID
Note that the Request ID will be displayed in the window that appears after transmitting the input. Make sure to note down this.
Input content post-transmission window
Search results display window
Reading period
Search results may be viewed up to 7 days after the execution of the search.
Last Updated:June 4, 2015
How do I interpret the search results? BLAST search
Search results are displayed in the following order.
  1. Precedence table of sequences with high homology scores
  2. Homologous sequences and their alignment
  3. Parameters and statistics
Note that the symbol “|” in the BLAST search results for nucleotide sequences indicates agreement between nucleotide sequences. For amino-acid sequences, matching amino acids will be displayed. The symbol “+” is used to indicate similarities between amino acids.

For further details, refer the original papers on BLAST.

BLAST Reference
Last Updated:June 4, 2015
A portion of the sequence that I entered was replaced with [N](X)! What happened? BLAST search
The sequence that you entered was filtered by the BLAST program. The filtering has the effect of replacing regions of your input sequence of low structural complexity with “N” (or “X” for amino-acid sequences). For details on filtering, see the section “Filtering” in the BLAST HELP. To disable filtering, select the OFF radio button in the “Filter” option in the lower portion of the Settings screen. Note with caution that setting this option to “OFF” may result in search times that are longer than normal.
Last Updated:June 3, 2015
What are the browser that the DDBJ service supports? ARSA BLAST NSSS PR search
DDBJ recommend using the following OS and browsers to use our servises.
DDBJ HP
OS:Windows7 or later , Mac OSX10.9 or later
Browser:Firefox latest versions , Chrome latest versions
DDBJ Nucleotide Sequence Submission System
Browser:Firefox , Chrome
D-way Submission System
Browser:Firefox latest version, Chrome latest version
BLAST / ARSA
OS:Windows7 or later , Mac OSX10.6 or later
Browser:IE10.X , IE9.X , Firefox , Chrome , Safari5.X or later
However, the OS, browser environment recommended above is subject to change without prior notice.
Last Updated:November 24, 2016
Regarding the E value displayed in the BLAST analysis results: How is this value calculated? BLAST search
The E value is computed using the following formula, in which l denotes the length of the query string, n denotes the number of strings stored in the database, and S is a score that measures the homology between nucleic acids or between amino acids. Note that k and m are positive constants. E=k*l*n*exp^(-mS) If the BLAST output results computed using this formula are displayed in the form 1E-X, this means that the quantity has the value 1.0*e^-X.
Last Updated:June 1, 2015
What rules govern the order in which BLAST search results are displayed? BLAST search
BLAST search results are displayed in descending order of homology score. There is no way to assign priorities to strings with identical scores, so there is no particular regularity to the order in which such strings are displayed.
Last Updated:June 1, 2015
The number of search results shown is too small! (I receive the message “No hit found.”) BLAST search
If the number of search results shown is fewer than the number specified for the options “Number of Search Results to Display” and “Number of Alignments to Display,” you may increase the number of displayed results by increasing the value of the “Expectation value” under the “Advanced settings” field. In such a case, try setting the expectation value to an extremely large number such as 10,000. Note that, if the string is too short (a sequence length of 10 or so), BLAST will frequently be unable to find matches.
Last Updated:June 1, 2015
ページの先頭へ戻る