Especially, it is good in that orthologous and paralogous relationship are identified from this database.
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| Cited from NAR |
Showing posts with label Paper. Show all posts
Showing posts with label Paper. Show all posts
2012-02-07
TreeFam: a curated database of phylogenetic trees of animal gene families
Treefam is a database for phylogenetic trees of animal gene families.
Especially, it is good in that orthologous and paralogous relationship are identified from this database.
Especially, it is good in that orthologous and paralogous relationship are identified from this database.
2011-11-17
The age of a single cell assembly
The age of a single cell assembly has become. Every assembler will be reconstructed to focus on the single cell assembly.
Picking up the pieces
Nature Methods 8, 896 (2011).
doi:10.1038/nmeth.1753
Author: Michael Eisenstein
An improved algorithm for genomic analysis allows scientists to build remarkably accurate and complete genomic sequences from single bacterial cells.
Annotation of the domestic dog genome sequence: finding the missing genes.
The sequencing the domestic dog genome with RNA-Seq technology!!
RNA-Seq.. Now, for genetic research, I don't know that RNA-Seq has to be implemented necessarily with NGS sequencing.
But, the money and time cost to analyze the data are the problem.
Annotation of the domestic dog genome sequence: finding the missing genes.
Mamm Genome. 2011 Nov 11;
Authors: Derrien T, Vaysse A, André C, Hitte C
Abstract
There are over 350 genetically distinct breeds of domestic dog that present considerable variation in morphology, physiology, and disease susceptibility. The genome sequence of the domestic dog was assembled and released in 2005, providing an estimated 20,000 protein-coding genes that are a great asset to the scientific community that uses the dog system as a genetic biomedical model and for comparative and evolutionary studies. Although the canine gene set had been predicted using a combination of ab initio methods, homology studies, motif analysis, and similarity-based programs, it still requires a deep annotation of noncoding genes, alternative splicing, pseudogenes, regulatory regions, and gain and loss events. Such analyses could benefit from new sequencing technologies (RNA-Seq) to better exploit the advantages of the canine genetic system in tracking disease genes. Here, we review the catalog of canine protein-coding genes and the search for missing genes, and we propose rationales for an accurate identification of noncoding genes though next-generation sequencing.
PMID: 22076420 [PubMed - as supplied by publisher]
2011-11-14
de Bruijn graph theory
Recently, de Bruijn graph theory has widely used in the filed of genome assembly.
Expecially, Velvet assembler is based on this graph theory.
The goal of De Bruijn graph is to make superstring through overlapping k - 1 suffix sequence.
So this concept can well match with assembly of short reads of a genome.
How can de Bruijn graph make a superstring?
Because de Bruijn graph is bidirectional graph, about some input information, it can make superstring as output through traveling every edges or node.
de Bruijn graph can be represented as one of between Hamiltonian cycle or Eulerian cycle.
Expecially, Velvet assembler is based on this graph theory.
The goal of De Bruijn graph is to make superstring through overlapping k - 1 suffix sequence.
So this concept can well match with assembly of short reads of a genome.
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| de Bruijn graph sample (cited from Wikipedia) |
How can de Bruijn graph make a superstring?
Because de Bruijn graph is bidirectional graph, about some input information, it can make superstring as output through traveling every edges or node.
de Bruijn graph can be represented as one of between Hamiltonian cycle or Eulerian cycle.
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