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...2692 days ago
2520 days ago
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...2921 days ago
2692 days ago
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...2201 days ago
2229 days ago
2982 days ago
1745 days ago
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...3906 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...2130 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ance...Tags: DUPCAR, Reconstructing, Contiguous, Ancestral, Regions, Duplications
2165 days ago
SDA: Long-read sequence and assembly of segmental duplications
Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs. ht...Tags: SDA, Long-read, sequence, assembly, segmental, duplications
1877 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...1549 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.html1963 days ago