> Tag > Links tagged with 'gene duplication'

Links tagged with 'gene duplication'

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IMCB - Fugu Genome ProjectTool Content

http://www.fugu-sg.org/ [open in a new window]

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Model Organisms > Databases
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.

links directory index: 1759
TitlePublication YearGoogle Scholar Citation Count
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes20021097
Fugu: a compact vertebrate reference genome2000108
Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning199980
Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome1993474
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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

S. pombe genomeDatabase Content

http://www.sanger.ac.uk/Projects/S_pombe/ [open in a new window]

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Model Organisms > Yeast

Schizosaccharomyces pombe Genome Sequencing Project.

links directory index: 1000
TitlePublication YearGoogle Scholar Citation Count
The genome sequence of Schizosaccharomyces pombe20021000
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tagsbase sequence centromere chromosome mapping dna sequence analysis eukaryotic cells fungal chromosomes fungal dna fungal genome fungal proteins gene duplication humans inborn genetic diseases introns schizosaccharomyces tertiary protein structure

MIPSDatabase Content

http://www.helmholtz-muenchen.de/en/ibis [open in a new window]

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Model Organisms > General Resources
Model Organisms > Other Organisms
Model Organisms > Plants
Model Organisms > Yeast
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.

links directory index: 703
TitlePublication YearGoogle Scholar Citation Count
MIPS: curated databases and comprehensive secondary data resources in 201020119
MIPS: analysis and annotation of proteins from whole genomes2004422
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics200487
MOsDB: an integrated information resource for rice genomics200317
Sputnik: a database platform for comparative plant genomics200350
The PEDANT genome database2003118
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tagsanimals arabidopsis arabidopsis proteins biological models complementary dna computational biology data mining dna transposable elements expressed sequence tags fungi gene duplication genetic databases genome genomics humans information storage and retrieval internet metabolomics mice micrornas neoplasm genes nucleic acid databases nucleic acid sequence homology oryza sativa phenotype plant genes plant genome protein binding protein databases protein interaction mapping protein sequence analysis proteins proteomics saccharomyces cerevisiae proteins sequence homology software systems integration user-computer interface

InParanoidDatabase Content

http://inparanoid.sbc.su.se/cgi-bin/index.cgi [open in a new window]

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Protein > Databases

The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.

links directory index: 612
TitlePublication YearGoogle Scholar Citation Count
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis201080
InParanoid 6: eukaryotic ortholog clusters with inparalogs2008127
Inparanoid: a comprehensive database of eukaryotic orthologs2005405
NAR Database Issue 2010
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tagsalgorithms animals bacterial genome cluster analysis computational biology database management systems escherichia coli eukaryotic cells gene duplication genetic databases genomics humans mice nucleic acid databases phylogeny protein databases proteins proteomics rats sequence homology tertiary protein structure

SelectomeDatabase Content

http://selectome.unil.ch/ [open in a new window]

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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.

links directory index: 53
TitlePublication YearGoogle Scholar Citation Count
Phylogenetic code in the cloud - can it meet the expectations?20102
Selectome: a database of positive selection200913
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes200838
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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

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp [open in a new window]

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Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
FGF: a web tool for Fishing Gene Family in a whole genome database20073
NAR Web Server Issue 2007
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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

SHORETool Content

http://1001genomes.org/downloads/shore.html [open in a new window]

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DNA > Mapping and Assembly
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Other Alignment Tools

SHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
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tagsadenocarcinoma arabidopsis base sequence bone neoplasms breast neoplasms chromosome mapping dna sequence analysis female frameshift mutation gene duplication genetic polymorphism humans middle aged molecular sequence data neoplasm metastasis nucleic acid sequence homology plant chromosomes plant dna plant genome sequence deletion thrombocytosis

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