BOL

BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA...

Align Synteny - Beginning from completed or draft genomes, find shared syntenic regions and align them quickly while accounting for inversions, rearrangements, and duplications. http://www2.decipher.codes/AlignSynteny.html

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language. The R package is distributed as platform independent source code under the GPL...

RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and...

GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data...

Bioinformatics online tutorial https://bioinformaticsonline.com/pages/view/1537/virtual-bioinformatics-online-tutorial #Bioinformatics #Tutorial

Bioinformatics for Beginners https://www.coursera.org/learn/bioinformatics which can help with learning the basics of the algorithms underpinning motif discovery.

Motif algorithms  This link on Nature explain: how does DNA sequence motif discovery work? Paper on BMC bioinformatics: survey of DNA motif finding algorithms This paper discusses some limitations and potentials of motif...

Understaning SAMtools http://www4.ncsu.edu/~rosswhet/BIT815/Overview/Week2/SAMformatAndCLtools.pdf 

Interesting plotting options in R https://www.r-graph-gallery.com/ #plot #graph #R

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...

Ribbon genomics http://genomeribbon.com/ #Visualization #Ribbon #Graph #Genome #BAM #SAM #Mummer

Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads...

Selfish genetic elements https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007700 #genetics #selfish #genome

lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...