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CusVarDB: A tool for building customized sample-specific variant protein database from Next-generation sequencing datasets

Authors: Sandeep Kasaragod; Varshasnata Mohanty; Ankur Tyagi; Santosh Kumar Behera; Arun H. Patil; Sneha M. Pinto; T. S. Keshava Prasad; +2 Authors

CusVarDB: A tool for building customized sample-specific variant protein database from Next-generation sequencing datasets

Abstract

CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and exome datasets. This repository will provide the resultant variant peptides identified in our study and its corresponding information. The detailed information of the table is given below. Supplementary Table 1. This table contains the resultant variant peptides along with its wild-type peptides from BT474, MDMAB157, MFM223, and HCC38 datasets. Along with mutant peptides, this section also provides additional information such as peptide-spectrum match (PSM), Protein accession, cross-correlation value from the search (Xcorr), and retention time (RT). Supplementary Table 2. This table provides the complete details of the resultant peptides. Here the mutant and corresponding wild-type peptides are mentioned in different sheets. For a given mutant peptide its wild-type peptide and corresponding information can be mapped using the VLOOKUP function in Excel by keeping column A (Sl.No) as lookup parameter. Supplementary Table 3. This table briefs about the variants which are already reported in other cancers.

Keywords

Next-generation Sequencing, Variant protein database, NGS-pipeline

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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Cancer Research