[ANNOUNCE] DNA Mutation Checker
heikki at ebi.ac.uk
Wed Feb 18 11:05:33 EST 1998
DNA Mutation Checker
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
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 /label: point
Feature /location: X58957; 155
Feature /change: g>c
Feature /re_site: +BsmAI; +Eco31I; -SfaNI
Feature /label: missense
Feature /region: coding
Feature /transl_table: 1
Feature /codon: agc>acc; 2
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.
______ _/ _/_____________________________________________________
_/ _/ 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
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