PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome A...912 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and sug...ed as hg38/GRCh38 human reference genome. if you map reads to GRCh38...: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_0000.../2017/11/13/which-human-reference-genome-t...1601 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconst...ncept of neighboring gene pairs. REGEN was designed to be used with any set of genomes...2315 days ago
ARCS: scaffolding genome drafts with linked reads
...d in linked reads to further organize draft genomes into highly contiguous assem...ow the contiguity of an ABySS H.sapiensgenome assembly can be increased ove...inked read data for connecting high-quality sequences in genome assembly drafts.2315 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single reference...that it can utilize multiple complete genomes of related organisms as refe...der and orient the contigs of a draft genome. In practical usage, our Mult...taset composed of several prokaryotic genomes...2315 days ago
Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all...this is the first method to detect breakpoint reads without using a reference genome....2313 days ago
SCUBAT: Scaffolding Contigs Using Blat And Transcripts
SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.2308 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein sequence sets. MMseqs2 is open source...Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of...2299 days ago
GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2300 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to j...inders from an adequate scaffolding evaluation are genome repeats. The previous standard for evaluation (Hunt et al., Genome B...2300 days ago