2012年5月31日星期四

developmental network models - a new evolutionary model for phenotypic variation

http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01649.x/abstract

We develop an explicit genenetwork model with three componentssome genes can receive environmental cues about the adult selective environmentsome genesthat interact repeatedly to determine each others’ final stateand other factors that translate these final expression states into thephenotypeWe show that the evolution of phenotypic plasticity is an important determinant of mutational patternsgenetic varianceandevolutionary potential of a populationPhenotypic plasticity tends to lead to populations with greater mutational variancegreater standinggenetic varianceandwhen the optimal phenotypes of two traits vary in concertgreater mutational and genetic correlationsHowever,plastic populations do not tend to respond much more rapidly to selection than do populations evolved in a static environmentWe find thatthe quantitative genetic descriptions of traits created by explicit developmental network models are evolutionarily labilewith genetic correlations that change rapidly with shifts in the selection regime.

a simulation work on deleterious mutations


Spatial heterogeneity in the strength of selection against deleterious alleles and the mutation load

tools for identifying repeat and transposons across the genomes


1. Identifying repeats and transposable elements insequenced genomeshow to find your way through the dense forest of programs



tools for detecting tandem repeat across genomes


Review of tandem repeat search toolssystematic approach to evaluating algorithmic performance


2012年5月30日星期三

impede - 阻碍

Inability to obtain accurate heritability estimates under natural conditions has impeded studies of behavioural trait evolution.

evoke the question - 导致了问题

evoke, cause

This evokes the question: how many individuals and how many times does each individual need to be measured to obtain a precise estimate of repeatability.

reformat the reference items in Word accompanied by ENDnote

see this figure, after remove field code, the secret references' links were masked and you can freely reformat your references. This is for Mac users.



Following is the example for windows users.

2012年5月26日星期六

some courses on computational biology/genomics

http://bcc.bx.psu.edu/courses/

VAAST - the Variant Annotation, Analysis and Search Tool

VAAST (the Variant AnnotationAnalysis and Search Toolis a probabilistic search tool for identifying damaged genesand their disease-causing variants in personal genome sequencesVAAST builds upon existing amino acidsubstitution (AASand aggregative approaches to variant prioritizationcombining elements of both into a single unifiedlikelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracyand inan easy-to-use fashionVAAST can score both coding and non-coding variantsevaluating the cumulative impact ofboth types of variants simultaneouslyVAAST can identify rare variants causing rare genetic diseasesand it can alsouse both rare and common variants to identify genes responsible for common diseasesVAAST thus has a muchgreater scope of use than any existing methodology.

Installing libsequence and analysis tools on OSX


Installing libsequence and analysis tools on OSX

VariScan

http://www.ub.edu/softevol/variscan/

population genetic tools for genome-scale dataincludingVariScan, the PERL PopGen modules, and the libsequenceC++ library.

predict SNP effects using R

Assessing whether point mutations introduce stop codons into chromosomal DNA using Ensembland R


perlmodinstall2 - Installing Perl Modules

http://www.rcbowen.com/imho/perl/modules.html

2012年5月24日星期四

concomitant increase - 伴随的增长

There was a concomitant increase in lifetime reproductive success as women whobegan their reproduction earlier generally had more children surviving toadulthood