[ANNOUNCE] DNA Mutation Checker

Heikki Lehvaslaiho heikki at ebi.ac.uk
Wed Feb 18 11:05:33 EST 1998


DNA Mutation Checker
-----------------------------------------------------------------
      http://www2.ebi.ac.uk/cgi-bin/mutations/check.cgi

DNA Mutation Checker program has been created to help researchers 
and database curators to verify the transription and translation 
effects of DNA level sequence variation.

The user is expected to give a valid reference sequence accession 
number, select the numbering system, and type in the start position 
of the change, followed by reference and variant nucleotide 
sequences.

The output gives details of the mutation and its effect in 
EMBL-like text format, e.g.:

ID           X58957:(132)+23G>C; translation: S8T
Description  point mutation in coding region
Description  causing an amino acid change
Feature      DNA
Feature        /label: point
Feature        /location: X58957; 155
Feature        /change: g>c
Feature        /re_site: +BsmAI; +Eco31I; -SfaNI
Feature      RNA
Feature        /label: missense
Feature        /region: coding
Feature        /transl_table: 1
Feature        /codon: agc>acc; 2
Feature      AA
Feature        /label: substitution
Feature        /location: 8
Feature        /change: S>T
//

The program reports the changed restriction enzyme sites for 
point mutations, affected mRNA region, shows the affected 
codon position and calculates the amino acid change. 
It is able to automatically detect the need for a non-standard 
translation table. The names in the ID lines follow the 
recommendations published in Antonorakis et al. 
Human Mutation 11:1-3(1998).

Mutation checker is a work under progress and offers currently 
only limited, simplistic analysis of the effects of mutations. 
Is not able to parse together separate exons in genomic clones, 
so it needs a cDNA reference sequence. The first coding region 
in the entry is used.

The checker program supposes that a mutation has no effect on 
mRNA processing. In some cases, the special role of the initiation 
codon is taken into account, but effects of termination codon 
mutations still need to be written in.

If you have comments or suggestions, please contact me.

The EBI Mutations page at http://www2.ebi.ac.uk/mutations/
contains general information on mutations and databases.

	-Heikki

______ _/      _/_____________________________________________________
      _/      _/                      http://www2.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________




More information about the Bio-soft mailing list