MTSNPScore is designed to score for polymorphic sites based on a number of parameters. Currently, it can score for mitochondrial polymorphisms but can be extrapolated to nuclear polymorphisms.The algorithm takes into account sites selected by the user as well as additional sites and their scores.

DETAIL DESCRIPTION IS AS FOLLOWS:

MTSNPScore generates the following:
1.) Patient scores and Genpat scores: Uses Genpat data as normal population for comparison on all parameters and provides scores for all genpat individuals for each patient
2.) Patient scores and Default normal scores: Uses normal Palan_Raj Indian population for comparison on all parameters: Scores assigned to all normal individuals for each patient
3.) Additional analysis report: This file provides output in two sections:
   (i) Common SNPs in high scoring patients are reported
   (ii) Exclusion of SNPs from this set that are also present in Normal individuals

This additional report provides help in manual assessment of the output.

There is provision to upload data on normal individuals and then this data is used to assign scores to patients
It is advised to upload normal data as sequence of complete Mitochondrial genomes. A set of inter-connected
PERL script is designed to extract the required features from the complete Mitochondrial genomes.

Hence forth, description of the various parameters and their usage is provided:-

1.) This web page is categorized into 23 broad parameters. Many of these comprise of various sub-parameters.

2.) As one can see, first 8 parameters display only score based on certain properties of the polymorphisms.

3.) Next 8 show variation data along with scores.

4.) The last 6 again display only scores and specific details of the polymorphism position along with age of onset if the disease and associated nuclear modifiers.

Invariant Peptides are also scored. For more information click the link!

5.) An important point to note is that we have categorized scoring scheme in two sections:
User defined and can be changed-> Depicted by green colored text-boxes
Default constant values-> Depicted by pink colored text-boxes.

6.) This tool despite being very comprehensive is easy to use and there is no limitation to the number of polymorphic sites as well as the number of individuals.

7.) To start with, default scores for CpG, SIFT, PolyPhen etc. are presented in boxes.Green colored text-boxes have score that can be modified by the user.

8.) Next comes genes that display base changes along with the scores associated with each change. The format of this is as follows:
example: In case of 12SrRNA, A663G#6 as one of the sites in the 'Additional sites' section. This shows a A-G change at position 663 with a score of 6.
User can add more sites or remove sites depending on disease under consideration.

9.) If user wants to skip a site in the given green boxes for genes, then he can assign a score of zero to such sites, values should not be deleted from these boxes.

10.) The Help file for MTSNPScore deals with the rationale behind selecting the default sites as well their scoring. User can click on the parameter for which detailed information is required. For viewing the entire Help file click on the main title.

A few parameters (for example: CpG, Initiation codon, Stop codon etc.) do not show anything when clicked. Just scroll the mouse over these links for their brief description.

11.) If no input file is specified the Index page reloads waiting for the user to upload file.

12.) There are no known bugs thus far, if anybody finds a bug kindly report it to kanwal_ash@ccmb.res.in