Structural variation: the hidden genomic treasure
...hing. CNVs are closely related to segmental duplications (SDs): SDs can stimulate the...riants (SVs) such as deletions, insertions, duplications, inversions and translocation...translocations, and unbalanced ones such as duplications and deletions (copy number va...2707 days ago
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mrFAST: Micro Read Fast Alignment Search Tool
...d mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with...2936 days ago
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Tools for Searching Repeats And Palindromic Sequences
...ter characterized and placed into five categories: Simple Repeats - Duplications of simple sets of DNA bases (...ally found at the centromeres and telomeres of chromosomes these are duplications of more complex 100-200 base...2216 days ago
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Bioinformatics -- Understanding of living systems through information science
...e changes through sudden mutations. Additionally, at the genome level, mutations called rearrangements, such as inversions, transpositions, and duplications, occur. The genome comparis...3921 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here m...2145 days ago
Structural variation: the hidden genomic treasure
Genome re-sequencing projects have revealed substantial amounts of genetic variation between individuals extending beyond single nucleotide polymorphisms (SNPs) and short indels. Structural Variations (SVs) and Copy Number Variations (CNVs) are a major source of genomic variation. However, compar...Tags: Bioinformatics, Chromosome, Genome, NGS, Structure Variation, Deletions, Insertions, Duplications, Inversions, Translocations
2707 days ago
Comment on "Genome in a Bottle (GIAB) Consortium"
..., as well as calls in difficult genomic contexts (e.g., homopolymers/tandem repeats and difficult-to-map regions like pseudogenes and segmental duplications). GIAB is also explorin...1564 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
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.html1978 days ago