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Old 01-10-2016, 01:39 PM   #1
kjpr
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Default Is there a way to compare the genomic locations of mutations for legacy transcripts w

Hi all
I have a list of variants described in hgvs format. The variants relate to old versions of transcripts. I want to translate these variants into genomic locations. I have previously used Mutalyzer to perform this task. However I am unable to perform this task using Mutalyzer with older versions of transcripts. So for example with the transcript

NM_003002.1:c.274G>T

There is no record returned in the current version of mutalyzer but there is for transcripts NM_003002.2, NM_003002.3.
Does anyone know how i might be able to return the genomic location for this old transcript version please.
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Old 01-10-2016, 01:57 PM   #2
lindenb
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see https://www.biostars.org/p/15992/ ; https://www.biostars.org/p/59340/ ;
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Old 01-11-2016, 10:42 AM   #3
m_two
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http://bioinformatics.mdanderson.org/main/Transvar

Introduction

TransVar is a reverse annotator for inferring genomic characterization(s) of mutations (e.g., chr3:178936091 G/A) from protein or cDNA annotation(s) (e.g., PIK3CA p.E545K or PIK3CA c.1633G>A). It is designed for resolving ambiguous mutation origins, arising from alternative splicing.

TransVar has the following features:

supports HGVS nomenclature
supports both left-alignment and right-alignment convention in reporting indels.
supports annotation of a region based on a transcript dependent characterization
supports single nucleotide variation (SNV), insertions and deletions (indels) and block substitutions
supports mutations at both coding region and intronic/UTR regions
supports transcript annotation from commonly-used databases such as Ensembl, NCBI RefSeq and GENCODE etc
supports UniProt protein id as transcript id
supports GRCh36, 37, 38
functionality of forward annotation.

Citation: Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K. TransVar: a multi-level variant annotator for precision genomics. Nature Methods. In Press.
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