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Links tagged with 'plant dna'

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Found 7 links

Displaying 7 links

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EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl [open in a new window]

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DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences200337
NAR Web Server Issue 2003
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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

iCE - internet Contig ExplorerTool Content

http://www.bcgsc.ca/platform/bioinfo/software/ice [open in a new window]

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DNA > Mapping and Assembly
Model Organisms > General Resources

Viewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps200321
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tagsanimals arabidopsis caenorhabditis caenorhabditis elegans contig mapping dna fingerprinting helminth dna humans mice molecular cloning oryza sativa plant dna rats

NEMBASE4Tool Content

http://www.nematodes.org/nembase4/ [open in a new window]

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Model Organisms > Worm
Sequence Comparison > Comparative Genomics

NEMBASE is a resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design.

links directory index: 335
TitlePublication YearGoogle Scholar Citation Count
A transcriptomic analysis of the phylum Nematoda2004163
NEMBASE: a resource for parasitic nematode ESTs200465
prot4EST: translating expressed sequence tags from neglected genomes200468
SimiTri--visualizing similarity relationships for groups of sequences200339
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tagsamino acid sequence homology animals arabidopsis artificial intelligence bacterial genome base composition base sequence benchmarking caenorhabditis elegans caenorhabditis elegans proteins chromosome mapping codon computational biology conserved sequence database management systems dna sequence analysis drosophila drosophila proteins expressed sequence tags gene expression profiling genetic databases genetic variation genome genomics helminth dna helminth genes horizontal gene transfer humans molecular evolution molecular sequence data nematoda parasites phylogeny plant dna plant genome protein biosynthesis protein databases proteins saccharomyces cerevisiae sequence alignment software design species specificity spirurida tertiary protein structure

Netgene2Tool Content

http://www.cbs.dtu.dk/services/NetGene2/ [open in a new window]

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Expression > Splicing

The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

links directory index: 447
TitlePublication YearGoogle Scholar Citation Count
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information1996447
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tagsalgorithms arabidopsis artificial intelligence exons expert systems factual databases forecasting genetic models green fluorescent proteins introns luminescent proteins molecular sequence data neural networks (computer) plant dna plant rna reproducibility of results rna precursors rna splicing

PatMatchTool Content

http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Protein > Domains and Motifs
RNA > Motifs

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

links directory index: 32
TitlePublication YearGoogle Scholar Citation Count
PatMatch: a program for finding patterns in peptide and nucleotide sequences200532
NAR Web Server Issue 2005
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tagsarabidopsis arabidopsis proteins dna sequence analysis peptides plant dna protein sequence analysis

PREP SuiteTool Content

http://prep.unl.edu/ [open in a new window]

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Model Organisms > Plants
RNA > Motifs

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

This content is being maintained by jpmower.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments200911
PREP-Mt: predictive RNA editor for plant mitochondrial genes200538
NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology base sequence binding sites chloroplast rna chloroplasts computational biology conserved sequence cytidine dna dna sequence analysis mitochondrial genes mitochondrial proteins molecular sequence data phylogeny plant dna plant gene expression regulation plant genes plant genome plant proteins protein binding protein databases reproducibility of results rna rna editing rna sequence analysis sensitivity and specificity sequence alignment statistical models

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
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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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