Virus typing

1. process

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.

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.

This system is used private division structure to manage results, so that only users in account mode can be used it.

2. usage

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 by numbers.
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.