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3937 days ago
Tools to detect synteny blocks regions among multiple genomes
...the same chromosome. These block regions have mostly been preserved by...onserved blocks and non-conserved regions to understand the mechanism a...ny server can be used for finding regions syntenic across multiple geno...pload files which contain synteny regions between two or more genomes a...2608 days ago
Public Databases for Bioinformatics !
...ct.org/files/ENCFF546PJU/@@download/ENCFF546PJU.bam, https://www.encodeproject.org/files/ENCFF059BEU/@@download/ENCFF059BEU.bam. Blacklisted regions were obtained from http:...1137 days ago
3416 days ago
Bioinformatics approach to Boar Taint
...s Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for calling SNPs and InDels inside previousy identified QTL regions on SSC5,13, and 7 with the ai...3787 days ago
3558 days ago
Genome Assembly Tools and Software - PART2 !!
...bly. The benefits of this approach include better assembled repetitive regions, less gaps and higher accurac...o; sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discov...2683 days ago
Awesome perl frameworks, libraries and software - PART 3
...ams in the terminal. mysociety/fixmystreet - This is mySociety's popular map-based reporting platform: easy to install in new countries and regions spencertipping/js-in-ten-min...2492 days ago
3940 days ago
Hidden Markov Models, Viterbi Algorithm, Markov Chain Exploration with script
...VB6) Problem : The CG island is a stretch of DNA (usually longer than 200 bases) in which the frequency of the CG sequence is higher than other regions. It is also called the CpG is...3822 days ago
3760 days ago
Conserved Domain Database (CDD) version 3.11 released
...t versions of RPS-BLAST (BLAST release 2.2.28 and up) using composition-based scoring. This abolishes the need to mask out compositionally biased regions in query sequences; Doma...3725 days ago
Special Project Scientist – Sorghum Genomics
...enting global genetic diversity Population genetic and genomic analyses, testing the hypothesis related to adaptation in multiple geographic regions Develop SNP assays from...3636 days ago
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3382 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2152 days ago
Perl script to find coding regions in DNA sequences
...hould be obtained with the two sequences: high values (positive) for coding protein sequences and low values (zero or even negative) for intronic regions. exon.fa >HUMHBB.2ex...2153 days ago
CAR: Reconstructing Contiguous Regions of an Ancestral Genome
We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts fo...Tags: Reconstruction, Contiguous, Regions, Ancestral, Genome, Bioinformatics, CAR
2542 days ago
Tags: SRBreak, Read-Depth, Split-Read, Framework, Breakpoints, Copy-Number, Variable, Regions
2180 days ago
Comment on "Basic command-line to run BLAST"
...e into smaller segments, called "words," and searching for matches to those words in the database. It then expands the matches to identify longer regions of similarity, called "alignm...418 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
...ized using tools such as Circos or SynMap. Interpret the results: Interpret the results of the synteny analysis by identifying conserved genomic regions, identifying gene families th...421 days ago