BOL

AB1 file format http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf #AB1 #File #Format

RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This...

BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the...

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc...

CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line. CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear...

Bioinformatics online tutorial https://www.gvl.org.au/learn/ #Tutorial #Online #Learn

Bioinformatics tutorial http://sepsis-omics.github.io/tutorials/ #Bioinformatics #Tutorial #Learn

Tab file to FASTA file $ awk '{print ">"$1"\n"$2}' allSeq_tm.txt > allSeq_tm.fa #Fasta #Tab #Convert #Tab2Fasta

KOBAS 3.0 is a web server for gene/protein functional annotation (Annotate module) and functional gene set enrichment(Enrichment module). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations...

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...

Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...

BioGPS opened 2016 with a publication in Nucleic Acids Research, right after the New Year holiday. Throughout the year, new designs for the site were being created, reviewed, adjusted, reviewed, adjusted, and more review/adjustments in anticipation...

http://www.bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf #Genome #Search #Mask

BAM2BED conversion bamToBed -i overall_exp_genome_rep1.bam > alignment.bed #Bed #bam #bamToBed #convert

Machine Learning books https://semanti.ca/blog/?the-most-important-machine-learning-books #books #machine #learn

First check the $SHELL ➜ Jit git:(master) echo $SHELL/usr/bin/zsh Then activate with source command ➜ Jit git:(master) source activate probeMining

➜ OligoMiner git:(master) conda create --name probeMining numpy scipy biopython scikit-learnSolving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/probeMining added / updated specs: - biopython - numpy -...

frodock: a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select...