*100710 CHOLINERGIC RECEPTOR, NICOTINIC, BETA POLYPEPTIDE 1; CHRNB1
;;CHRNB;;
ACETYLCHOLINE RECEPTOR, MUSCLE, BETA SUBUNIT; ACHRB
*FIELD* AV
.0001
MYASTHENIC SYNDROME, CONGENITAL, SLOW-CHANNEL
CHRNB1, VAL266MET
In a 19-year-old female with slow-channel congenital myasthenic syndrome
(601462), Engel et al. (1996) identified a heterozygous 796G-A
transition in exon 8 of the CHRNB1 gene, resulting in a val266-to-met
(V266M) substitution in a conserved residue in the M2 transmembrane
domain of the AChR-beta subunit. Functional expression studies showed
that the V266M mutation slowed the rate of AChR channel closure and
increased the apparent affinity for ACh. The mutation also caused
pathologic channel openings even in the absence of ACh, resulting in a
leaky channel. Cationic overload of the postsynaptic region caused an
endplate myopathy.
.0002
MYASTHENIC SYNDROME, CONGENITAL, SLOW-CHANNEL
CHRNB1, LEU263MET
In a 32-year-old male with slow-channel congenital myasthenic syndrome
(601462), Gomez et al. (1996) identified a heterozygous C-to-A
transversion in the CHRNB1 gene, resulting in a leu263-to-met (L263M)
substitution. Functional expression studies showed that the L263M
mutation interrupted the leucine ring of the AChR channel gate, causing
an 8-fold increase in channel open time and resulting in severe endplate
myopathy and extensive remodeling of the postsynaptic membrane. The
pronounced abnormalities in neuromuscular synaptic architecture and
function and the muscle fiber damage and weakness resulting from a
single point mutation were a dramatic example of a mutation having a
dominant gain of function and of hereditary excitotoxicity.
.0003
MYASTHENIC SYNDROME, CONGENITAL, ASSOCIATED WITH ACETYLCHOLINE RECEPTOR
DEFICIENCY
CHRNB1, 9-BP DEL, NT1276
In 3 sibs with congenital myasthenia and AChR deficiency (608931),
Quiram et al. (1999) identified compound heterozygosity for 2 mutations
in the CHRNB1 gene. One mutation was a 9-bp deletion (1276del9) in exon
10, resulting in a deletion of 3 codons (426-428) in the long
cytoplasmic loop between the M3 and M4 domains of the protein. The
second mutation was a skipping of exon 8 (100710.0004), truncating the
beta subunit before its M1 transmembrane domain and abolishing surface
expression of pentameric AChR. By coexpressing the 3-codon deleted
subunit with combinations of wildtype subunits in HEK293 cells, Quiram
et al. (1999) demonstrated that the mutation impairs AChR assembly by
disrupting a specific interaction between the beta and delta (100720)
subunits. Studies with related deletion and missense mutations indicated
that secondary structure in this region of the beta subunit is crucial
for interaction with the delta subunit. The findings implied that the
mutated residues are positioned at the interface between beta and delta
subunits and demonstrated contribution of this local region of the long
cytoplasmic loop to AChR assembly.
.0004
MYASTHENIC SYNDROME, CONGENITAL, ASSOCIATED WITH ACETYLCHOLINE RECEPTOR
DEFICIENCY
CHRNB1, EX8DEL
See 100710.0003 and Quiram et al. (1999).
*FIELD* SA
Beeson et al. (1989)
*FIELD* RF
Hi,
If there exist multiple pattern in a file, how can I find the last record matching the pattern through perl.
The below script searches for the pattern everywhere in an input file.
#! /usr/bin/perl -s -wnl
BEGIN {
$pattern or
warn"Usage: $0 -pattern='RE' \n" and
exit 255;... (5 Replies)
Dear All
I have a file like this
112534554
446538656
444695656
225696966
226569744
228787874
113536566
443533535
222564552
115464656
225445345
225533234
I want to cut the file into different parts where the first two columns are '11' . The first two columns will be either... (3 Replies)
Hi
I have a file (say 'file1')and I want to search for a first occurence of pattern (say 'ERROR') and print ten lines in the file below pattern. I have to code it in PERL and I am using Solaris 5.9.
I appreciate any help with code
Thanks
Ammu (6 Replies)
Hi,
I am new to ksh scripting and I have a problem.
I have a file in which I have to search for a particular pattern say 'a' then from that line I need to search for another pattern say 'b' in the previous lines and thne print the file from pattern 'b' till the end of file.
For eg:
... (2 Replies)
i have a file as below
sample.pl
parameter1
argument1
argument2
parameter2
I want out as below
argument1
argument2
that is , i want to print all the lines between parameter1 & parameter 2.
i tried with the following
if($mystring =~ m/parameter1(.*?)parameter2/) (2 Replies)
Hello,
I'm new to this forum. I've been doing a lot of sed work lately and have found many useful tips on this forum. I've hit a roadblock in a project, though, and could really use some help.
I have a text file with many lines like the following, i.e., some lines begin with a single word... (3 Replies)
Hi all,
on Solaris 10, I'd like to print a range of lines starting at pattern but also including the very first line before pattern.
the following doesn't print the range starting at pattern and going down to the end of file: cat <my file> | sed -n -e '/<pattern>{x;p;}/'
I need to include the... (1 Reply)
Hi,
I have script like below:
#!/usr/local/bin/perl
use strict;
use warnings;
while (<DATA>) {
( my ($s_id) = /^\d+\|(\d+?)\|/ ) ;
if ( $s_id == 1 ){
s/^(.*\|)*.*ABC\.pi=(+|+)*.*ABC\.id=(\d+|+).*$/$1$2|$3/s;
print "$1$2|$3\n"; (2 Replies)
hello everyone,
im new here, and also programming with awk, sed and grep commands on linux.
In my text i have many lines with this config:
1 1 4 3 1 1 2 5
2 2 1 1 1 3 1 2
1 3 1 1 1 2 2 2
5 2 4 1
3 2 1 1 4 1 2 1
1 1 3 2 1 1 5 4
1 3 1 1... (3 Replies)
Hello,
I have below format log file,
Comparing csv_converted_files/2201/9747.1012H67126.5077292103609547345.csv and csv_converted_files/22019/97447.1012H67126.5077292103609547345.csv
Comparing csv_converted_files/2559/9447.1012H67126.5077292103609547345.csv and... (6 Replies)
Discussion started by: arvindshukla81
6 Replies
LEARN ABOUT DEBIAN
bio::seqevolution::dnapoint
Bio::SeqEvolution::DNAPoint(3pm) User Contributed Perl Documentation Bio::SeqEvolution::DNAPoint(3pm)NAME
Bio::SeqEvolution::DNAPoint - evolve a sequence by point mutations
SYNOPSIS
# $seq is a Bio::PrimarySeqI to mutate
$evolve = Bio::SeqEvolution::Factory->new (-rate => 5,
-seq => $seq,
-identity => 50
);
$newseq = $evolve->next_seq;
DESCRIPTION
Bio::SeqEvolution::DNAPoint implements the simplest evolution model: nucleotides change by point mutations, only. Transition/transversion
rate of the change, rate(), can be set.
The new sequences are named with the id of the reference sequence added with a running number. Placing a new sequence into a factory to be
evolved resets that counter. It can also be called directly with reset_sequence_counter.
The default sequence type returned is Bio::PrimarySeq. This can be changed to any Bio::PrimarySeqI compliant sequence class.
Internally the probability of the change of one nucleotide is mapped to scale from 0 to 100. The probability of the transition occupies
range from 0 to some value. The remaining range is divided equally among the two transversion nucleotides. A random number is then
generated to pick up one change.
Not that the default transition/transversion rate, 1:1, leads to observed transition/transversion ratio of 1:2 simply because there is only
one transition nucleotide versus two transversion nucleotides.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
CONTRIBUTORS
Additional contributor's names and emails here
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
seq
Title : seq
Usage : $obj->seq($newval)
Function: Set the sequence object for the original sequence
Returns : The sequence object
Args : newvalue (optional)
Setting this will reset mutation and generated mutation counters.
set_mutated_seq
Title : seq_mutated_seq
Usage : $obj->set_mutated_seq($newval)
Function: In case of mutating a sequence with multiple evolvers, this
Returns : set_mutated_seq
Args : newvalue (optional)
rate
Title : rate
Usage : $obj->rate($newval)
Function: Set the transition/transversion rate.
Returns : value of rate
Args : newvalue (optional)
Transition/transversion ratio is an observed attribute of an sequence comparison. We are dealing here with the transition/transversion rate
that we set for our model of sequence evolution.
Note that we are using standard nucleotide alphabet and that there can there is only one transition versus two possible transversions. Rate
2 is needed to have an observed transition/transversion ratio of 1.
next_seq
Title : next_seq
Usage : $obj->next_seq
Function: Evolve the reference sequence to desired level
Returns : A new sequence object mutated from the reference sequence
Args : -
mutate
Title : mutate
Usage : $obj->mutate
Function: mutate the sequence at the given location according to the model
Returns : true
Args : integer, start location of the mutation, required argument
Called from next_seq().
perl v5.14.2 2012-03-02 Bio::SeqEvolution::DNAPoint(3pm)