This is a analysis pipeline for estimating subtype/genotype of virus from
its sequence. Once a user submit a query sequence, the following steps
are done automatically.
This system is used private division
structure to manage results, so that only users in
account mode can be used it.
- A query sequence is aligned against the
reference sequence to identify the location of the query on the genome.
- Sequence fragments corresponding to the location are clipped out from
genome entries whose genotypes/subtypes are well identified.
- The sequences with the query are multiple-aligned, and genetic distances
and a phylogenetic tree are estimatd.
- Boostrap re-sampling is done if the re-sampling number is estimated.
2.1. job submission
The job submission form is displayed if you click 'Execution' link under
'Virus typing' phrase. You can set a query sequence by uploading a FASTA
format file or by copying & pasting it to the text field. If you
would like to add notation to the job, you can type the field in.
The followings are optional parameters.
- alignment program
Ether 'lalign' or 'lfasta' can be selected, although 'lalign' is recommended.
- minimum length of matching region
If the query sequence does not have longer match to the reference (genome)
sequence than the length, the further analysis is not done. This means that
queries which have too low homology (or no homology) to reference sequence
cannot be processed.
Please notice that the minimum length should be specifiedy by the percentage
(%) of the query length.
- number of bootstrap re-sampling
If you type a number in this field, bootstrap re-sampling analysis will be done
after standard phylogenetic analysis.
2.2. view results
Correctly finished results are listed up if you click 'Show results' link under
'Virus typing' phrase. After selecting a result and data type (map or tree),
you can see the result by clicking go' button.
2.2.1. result-1 : map
If you choose 'map' as a data type, the location of the query on the genome is
displayed graphically. The style of this page is just like
Map viewer. Instead of a map information, the query
location is drawn by horizontal line and position of both ends are displayed
The graphic can also be displayed by JPEG image file by clicking
'[image mode]' link.
2.2.2. result-2 : tree
If you choose 'tree' as a data type, the relationship of the query (designed
by 'query') and fragments from genomes whose genotypes/subtypes are well
identified is displayed. The resulted phylogenetic tree is displayed by
use of Tree viewer.
2.3. job status
Current status of virus typing jobs are displayed if you click 'Job status'
link under 'Virus typing' phrase. If the error has occured during the
analysis, the intermediate file of the process can be seen.
This page is also used to remove unnecessary results.