Results for "structural and sequence variation"
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A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial g...2582 days ago
CLA: Contig-Layout-Authenticator
To improve upon the shortcomings associated with the construction of dr...also hints at probable misassemblies and contaminations, for the users...draft. The CLA pipeline was designed and trained extensively on various bac...g tools using both simulated and real sequence...2581 days ago
- This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools t...assemblies of bacterial sequence data. The bacterial samp...eaning that there are forward and reverse reads, which we will desig...ob/master/Genome%20Assembly%20and%20Ann...
2581 days ago
A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
PAGIT addresses the need for software to generate high quality draft genomes. It is...bler. iCORN, that enables errors in the consensus sequence to be corrected by iterativel...the latest assembly. PAGIT bundles these software and makes...2573 days ago
CABOG: Celera Assembler with Best Overlap Graph
CABOG (Celera Assembler with Best Overlap Graph) is scientific...the first draft human genome sequence. The software was releas...letters per read that modern sequencers provide. What these program...oceans (Sargasso Sea in 2004 and Global Ocean Sampling in 2007). It...2571 days ago
NCBI Prokaryotic Genome Annotation Pipeline
NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). Genome annotation...enes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobil...sp;the pipeline in NCBI Handbook c...2570 days ago
CAR: Reconstructing Contiguous Regions of an Ancestral Genome
We describe a new method for predicting the ancestral order and orientation of those interval...of the available human genome sequence data. The precision is f...mmalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that...2568 days ago
- The process of finishing a genome and moving it from a draft&n...e genomes is more challenging and often draft genomes are fragm...ed the use of optical mapping and mate-pair data to augment assembli...multiple maps, contig graphs and scaffolds. Augmenting assem...
2565 days ago
AVID: A Global Alignment Program
A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large geno...t of large syntenic genomic regions and whole genome human/mouse alignment...or the representation of alignments and metho...2562 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grin...proteomic, metaproteomic shotgun and amplicon datasets from current seq...ernative sequencing methods for a sequence-...2562 days ago
