Results for "fragments"
Blogs
Tools to detect synteny blocks regions among multiple genomes
...genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship...2626 days ago
Dynamic chromosome breakpoints !!!
...contributed in development of new species. I will try to explain the genome hotspots/Evolutionary Breakpoint Regions(EBRs)/fragile regions/weak fragments/ in my next blog. Soft...3568 days ago
- +3 more Blogs
Bookmarks
RACA: Reference-Assisted Chromosome Assembly
...Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome info...2967 days ago
- ...ncy reduction: detection and selectively removal of redundant contigs from an initial de novo assembly scaffolding: joining of genome fragments using paired-end and/or mate-...
2819 days ago
- +10 more Bookmarks
Pages
Genome Assembly Tools and Software - PART2 !!
...mosome AssemblyRACA is an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome info...2701 days ago
Top-level pages
List of In-silico Binding Site Prediction Tools
...ional surfaces of >19,000 structures in the SplitPocket (http://pocket.uchicago.edu/). The pairwise alignment of the unbound and split-pocket fragments is superimposed to evaluate t...3760 days ago
Commercial and public next-gen-seq (NGS) software
...which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a...or ChIP-Seq. MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter th...3535 days ago
- +5 more Top-level pages
News
- ...se of hundreds of biomarkers that are then easily detectable in a patient's urine. The MIT nanoparticles are coated with peptides (short protein fragments) targeted by different MMPs....
3737 days ago
Video
- ...NA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms when hybridized to restriction digests, or specific fragments, of an individual's DNA. The...
3889 days ago
Bio-Scripts
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1381 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the intronic region. gunzip -c...1381 days ago
- +1 more Bio-Scripts
Tags
- TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a desktop computer, therefore allowing researchers ...
Tags: TACOA, Taxonomic, classification, environmental, genomic, fragments, KNN, Contamination
2198 days ago
- AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignm...
Tags: AnchorWave, Anchored, Wavefront, Alignment, collinear, regions, conserved, anchors, CDS, exon, currently, breaks, collinear, regions, fragments, anchor, inter-anchor, intervals
818 days ago
Comments
Comment on "LAMSA: fast split read alignment with long approximate matches"
...ad [INT] Number of threads. [1] -l --seed-len [INT] Length of seeding fragments. [50] -i --seed-inv [INT] Distance between neighboring seeding fragments. [100] -p --max-loci [INT] Ma...2138 days ago
