Mercurial > repos > saketkc > condel
comparison tools/condel/condel_web.xml @ 0:742c7ee37f8b
push
author | Saket Choudhary <saketkc@gmail.com> |
---|---|
date | Wed, 20 Nov 2013 00:48:30 +0530 |
parents | |
children | 5915ae11d9cd |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:742c7ee37f8b |
---|---|
1 <tool id="condel_web" name="condel"> | |
2 <description>Condel web service</description> | |
3 <command interpreter="python"> | |
4 condel_web.py --input $input --output $output | |
5 </command> | |
6 <inputs> | |
7 <param name="input" format="text" type="data" label="Input Variants" /> | |
8 </inputs> | |
9 <outputs> | |
10 <data name="output" format="tabular"/> | |
11 </outputs> | |
12 <help> | |
13 **What it does** | |
14 Condel stands for CONsensus DELeteriousness score of non-synonymous single nucleotide variants (SNVs). | |
15 The idea behind it is to integrate the output of computational tools aimed at assessing the impact of non synonymous | |
16 SNVs on protein function. To do this, it computes a weighted average of the scores (WAS) of these tools. | |
17 Condel was developed to integrate the outputs of five tools: SIFT, Polyphen2, MAPP, LogR Pfam E-value | |
18 (implemented ad hoc following the instructions at Clifford RJ, Edmonson MN, Nguyen C, and Buetow KH (2004) | |
19 Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics 20, 1006-1014) and MutationAssessor | |
20 | |
21 | |
22 The scores of different methods are weighted using the complementary cumulative distributions produced by the five | |
23 methods on a dataset of approximately 20000 missense SNPs, both deleterious and neutral. | |
24 The probability that a predicted deleterious mutation is not a false positive of the method and the probability that a | |
25 predicted neutral mutation is not a false negative are employed as weights | |
26 | |
27 **Citation** | |
28 | |
29 If you use this Galaxy tool in work leading to a scientific publication please cite: | |
30 | |
31 Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, | |
32 Condel (2011) Abel González-Pérez and Nuria López-Bigas, American Journal of Human Genetics 10.1016/j.ajhg.2011.03.004 | |
33 </help> | |
34 </tool> | |
35 |