IVDB BLAST Help

Local sequence alignment software comparing user-supplied data (e.g. WorkSet) with IVDB's built-in databases


About BLAST

BLAST (Basic Local Alignment Search Tool) is developed in the 1990s by four scientists at NCBI to facilitate the search for a specific sequence in a sequence database which resembles a given sequence. This resemblance may be defined by the user through some input parameters.

BLAST in five steps:

1. Specify the program you want to use.

There are six types of search you can perform, each corresponds to a different program:

  • blastn compares a nucleotide sequence against a nucleotide sequence database.
  • blastp compares an amino acid sequence against a protein sequence database.
  • blastx compares a nucleotide sequence which is translated in all six frames against a protein sequence database.
  • tblastn compares a protein sequence against a six-frame translation nucleotide sequence database.
  • tblastx compares a six-frame translated nucleotide sequence against a six-frame translated nucleotide sequence database. This method is the slowest.
  • PSI-tblastn performs the same comparison as tblastn except it uses a Position Specific Iterative method.

2. Choose the target database.

After you have chosen the appropriate program, all databases corresponding to the program will become selectable, the default database is the nr database.

3. Specify the source sequence to be compared.

Your source sequence can be loaded in many ways: either directly through your WorkSet, or type/paste it manually or by loading a fasta file stored in your computer.

4. Specify the output file.

You can define your own file name here. The default output name is NuWorkset.aln.

5. Use advanced features.

You can click the little arrow on the right corner of the 'Advanced' bar to show more options. Detailed explanation following each option is available.

Blast result

BLAST searches are handled by supercomputers in BIG for high-performance computation. As one search might take some time, the result page will refresh every three seconds. You can take this a break and to have a cup of coffee. Once the comparison is done, you can download the result file and save it on your computer.


IVDB is supported by institutional grant from Beijing Institute of Genomics, CAS  Feedback