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Links tagged with 'vertebrates'

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FFPredTool Content

http://bioinf.cs.ucl.ac.uk/ffpred/

Protein > Annotation and Function
Protein > Sequence Features

Using a machine learning approach, FFPred server predicts protein function using protein features scanned against a library of over 300 Gene Ontology annotation terms. FFPred has the capacity to annotate distant homologues and orphan protein sequences.

NAR Web Server Issue 2008
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tagsanimals humans mice protein sequence analysis proteome systems integration vertebrates

GENSCANTool Content

http://genes.mit.edu/GENSCAN.html

DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

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tagsanimals dna dna sequence analysis exons genes genetic models genetic promoter regions genetic techniques genetic transcription human genome humans introns markov chains molecular sequence data nucleic acid repetitive sequences probability protein biosynthesis proteins rna splicing vertebrates

IMCB - Fugu Genome ProjectTool Content

http://www.fugu-sg.org/

Model Organisms > Fish

Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annotation tools, an Ensembl mirror, and BLAST.

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tagsanimals base sequence biological evolution computational biology conserved sequence cosmids dna dna sequence analysis dna transposable elements exons factual databases fish proteins fishes gene duplication gene library gene order genetic models genome genomics human genome humans introns japan mammals microsatellite repeats molecular evolution molecular sequence data nucleic acid repetitive sequences open reading frames phylogeny physical chromosome mapping poisonous fishes proteins proteome research satellite dna sequence alignment synteny takifugu vertebrates

OrthoDBDatabase Content

http://cegg.unige.ch/orthodb

Protein > Databases

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across 44 vertebrates, 25 arthropods, and 46 fungi. OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive orthology database querying.

NAR Database Issue 2011
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tagsamino acid sequence homology animals arthropods drosophila melanogaster fungi genes genetic databases genomics mice molecular evolution molecular sequence annotation phylogeny proteins saccharomyces cerevisiae tertiary protein structure vertebrates

SelectomeDatabase Content

http://selectome.unil.ch/

Protein > Databases
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences

Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.

This content is being maintained by selectome.

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tagsamino acid sequence homology animals codon computational biology computing methodologies gene duplication genes genetic databases genetic selection medical informatics applications phylogeny proteins software design vertebrates

SynoRTool Content

http://synor.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SynoR searches vertebrate genomes for synonymous regulatory elements.

NAR Web Server Issue 2005
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tagsanimals binding sites cardiac myocytes gene expression regulation genomics humans mice rats response elements transcription factors vertebrates

Vega Annotation BrowserTool Content

http://vega.sanger.ac.uk

Human Genome > Annotations
Model Organisms > Fish
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality curation of finished sequence.

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tagsanimals chromosome mapping dna sequence analysis genetic databases vertebrates