BOL

PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different...

samtools view -f 256 Input.bam | awk '$6 ~/S/ && $7 == "=" {print $0}' > Secondary_clipped.sam

The easiest way to get Alfred is to download a statically linked binary from the Alfred github release page. Alternatively, you can build Alfred from source. Alfred dependencies are included as submodules so you need to do a recursive...

Bioinformatics jobs at http://svimsbic.org/SRF_Notification.pdf #SVIMSBIC #Bioinformatics

BioCircos.js is an open source interactive Javascript library which provides an easy way to interactive display biological data on the web. It implements a raster-based SVG visualization using the open source Javascript...

git basic commands https://confluence.atlassian.com/bitbucketserver/basic-git-commands-776639767.html #git #commands #gitcommand

what may be the cause that ΔΔG value in I-mutant and iStable server different for same mutation, when the predictor for iStable is I-mutant? I-mutant ΔΔG value is -2.12 iStable ΔΔG value...

To facilitate bilateral cooperation in biotechnology between the scientific communities of India and Germany, the Department of Biotechnology (DBT) will soon begin collaborative research in the identified priority area of 'Bioinformatics in Health...

HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and (iii) is fully automated (requires...

GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can...

Assessing an effective undergraduate module #teaching applied #bioinformatics to biology students http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005872

get the fasta genes using gff3 and genome.fa sequence: ~/Tools/bedtools2/bin/bedtools getfasta -fi vaga.fa -bed Adineta_vaga.v2.gff3 -fo Adineta_vaga_genes.fa

move to ~/.sshcd ~/.sshchmod 400 ~/.ssh/id_rsayou can add the config file to easy access.

FILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\n" }'perl -pe '$_ .= "\n"'perl -pe 's/$/\n/'perl -nE 'say' # Double space a file, except the blank linesperl -pe '$_ .= "\n" unless /^$/'perl -pe '$_ .= "\n" if...

Dot, an interactive dot plot viewer that allows genome scientists to visualize genome-genome alignments in order to evaluate new assemblies and perform exploratory comparative genomics.  Dot supports the output of MUMmer’s nucmer aligner...

Graph visualization with R http://www.bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.pdf #R #Graph #Gviz #Visualisation

https://www.mitomap.org/MITOMAP -A compendium of polymorphisms and mutations in human mitochondrial DNA #mtDNA #DBs