BLAST/FASTA similarity searches
1. usage
1.1. job submission
There are four submission pages, which correspond to the combination of program
types (BLAST and FASTA) and molecular types (nucleic and amino acid databases).
1.1.1. mandatory parameters
- program
The following programs can be selected.
| BLAST | nucleic acid DB |
blastn, tblastn, tblastx |
| amino acid DB | blastp, blastx |
| FASTA | nucleic acid DB |
fasta |
| amino acid DB | fasta |
- database
You need to choose one or more databases from Hepatitis virus C, B, and E
databases.
- query sequence
You can set a query sequence by uploading a FASTA format file or by copying
& pasting it to the text field.
- output
You need to specify E-mail address to which the search result will be returned.
If you are in account mode, you can keep
the results in the database server by checking the corresponding checkbox.
In this case, you need not type E-mail address in.
1.1.2. optional parameters - BLAST
The following parameters can be set.
- number of scores
- number of alignment
- if making gapped alignment
- expectation value threshold
- wordsize
- if query filter on
If you have to set other BLAST parameters than above, you can set them
in 'other parameters' field by BLAST command line style.
1.1.3. optional parameters - FASTA
The following parameters can be set.
- number of scores
- number of alignment
- K-tuple number
If you have to set other FASTA parameters than above, you can set them
in 'other parameters' field by FASTA command line style.
1.2. view results
If you execute similarity searches in account
mode and setting to keep results on the server, you can see a list of
job status and results by clicking 'Show result' link under the 'Similarity
search' phrase. You can see a result by clicking corresponding Job ID.
This page is also used to remove unnecessary results.