Table of Content
Databases
Genome Browser
length information of human chromosomes
http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=1230&chromInfoPage=
- [http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=1230&chromInfoPage= Lengths of human chromosomes]
Ensembl
general
biomart
Automatic fetching of gene annotation, structure, function. Comparative genomics analysis.
R package
mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
getGene(id = 'CD44', type = "hgnc_symbol", mart = mart)
genebuild
[http://www.ensembl.org/info/docs/genebuild/genome_annotation.html reference]
Ensembl transcripts displayed on our website are products of the Ensembl automatic pipeline, termed the Ensembl genebuild.
All Ensembl transcripts are based on experimental evidence and thus the automated pipeline relies on the mRNAs and protein sequences deposited into public databases from the scientific community.
Exonerate is a tool for pairwise sequence comparison, used in the Ensembl genebuild to align mRNA to the assembly.
Regulatory Build
Promoters are not available for most genes in Ensembl.
One can find information on genome-wide studies of regulatory regions in Ensembl Regulatory Build.
VEGA database
The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence.
Human, mouse and zebrafish are in the process of being completely annotated.
In other species, the annotation is only of specific genomic regions of particular biological interest.
Consensus CDS (CCDS) project
The CCDS project is a collaborative effort to identify a core set of protein coding regions that are consistently annotated and of high quality.
Initial results from the Consensus CDS (CCDS) project are now available through the appropriate Ensembl gene pages and from the CCDS project page at NCBI.
Applications
Homology search
Next-Gen Sequencing
Computing
Phylogenetic tree
R package: phangorn
- [http://cran.r-project.org/web/packages/phangorn/index.html Souce code]
- Estimating phylogenetic trees with phangorn [http://cran.univ-lyon1.fr/web/packages/phangorn/vignettes/Trees.pdf PDF]
- Special features of phangorn [http://cran.r-project.org/web/packages/phangorn/vignettes/phangorn-specials.pdf PDF]
- Paper: [http://bioinformatics.oxfordjournals.org/content/27/4/592 phangorn: phylogenetic analysis in R]
- Presentation [http://rug.mnhn.fr/semin-r/PDF/semin-R_phylogenetics_KSchliep_180310.pdf PDF]
Other
- [http://evolution.genetics.washington.edu/phylip.html PHYLIP]
- [http://discover.nci.nih.gov/matchminer/index.jsp MatchMiner] is a set of tools that enables the user to translate between disparate ids for the same gene.
- [http://main.g2.bx.psu.edu/ Galaxy]
- [http://genometools.org/index.html GenomeTools: versatile open source genome analysis software]
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