> Tag > Links tagged with 'plant genome'

Links tagged with 'plant genome'

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GeneSplicerTool Content

http://cbcb.umd.edu/software/GeneSplicer/ [open in a new window]

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Expression > Splicing

A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice.

links directory index: 233
TitlePublication YearGoogle Scholar Citation Count
GeneSplicer: a new computational method for splice site prediction2001233
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tagsalgorithms alternative splicing arabidopsis computational biology dna factual databases genes human genome humans plant genome

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/ [open in a new window]

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DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

links directory index: 276
TitlePublication YearGoogle Scholar Citation Count
The ITS2 Database III--sequences and structures for phylogeny201038
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses200667
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures200559
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota2005112
NAR Web Server Issue 2006
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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

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

OligoArrayTool Content

http://berry.engin.umich.edu/oligoarray2_1/ [open in a new window]

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Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > General Resources

OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequenced genome can be found at http://berry.engin.umich.edu/oligoarraydb/index.html

links directory index: 236
TitlePublication YearGoogle Scholar Citation Count
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach2003236
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tagsalgorithms arabidopsis gc rich sequence gene expression profiling genetic transcription nucleic acid conformation oligonucleotide array sequence analysis oligonucleotide probes plant genome thermodynamics

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

RJPrimersTool Content

http://probes.pw.usda.gov/RJPrimers/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench

RJPrimers is a web-based server that allows for accurate identification of unique repeat junctions using BLASTN against annotated repeat databases and a repeat junction finding algorithm. It also computes repeat junction-based primer design using Primer3 and BatchPrimer3.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development20103
NAR Web Server Issue 2010
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tagsdna primers genetic markers interspersed repetitive sequences oryza sativa plant genome poaceae polymerase chain reaction

RPBSResource Content

http://bioserv.rpbs.jussieu.fr/ [open in a new window]

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Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Biochemical Features
Protein > Sequence Features

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

This content is being maintained by jompo.

links directory index: 852
TitlePublication YearGoogle Scholar Citation Count
RPBS: a web resource for structural bioinformatics200520
Filtering redundancies for sequence similarity search programs20053
Local backbone structure prediction of proteins200443
New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification1999103
PredAcc: prediction of solvent accessibility199945
A global taxonomy of loops in globular proteins199684
Automat and BLAST: comparison of two protein sequence similarity search programs19952
Automat: a novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS19948
Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences1987544
NAR Web Server Issue 2005
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tagsacquired immunodeficiency syndrome algorithms amino acid sequence amino acid sequence homology amino acids animals arabidopsis autoimmune diseases azurin bacterial genome chemical models computational biology computer simulation computer-assisted numerical analysis consensus sequence database management systems dna dna sequence analysis evaluation studies as topic factual databases genetic databases globins glycine hiv humans hydrolases leghemoglobin logistic models methods molecular models molecular sequence data nucleic acid sequence homology plant genome plastocyanin protein conformation protein structural homology proteins rats reproducibility of results secondary protein structure sequence alignment sequence analysis sequence homology solvents thiosulfate sulfurtransferase

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

The Arabidopsis Information Resource (TAIR)Resource Content

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

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Model Organisms > Plants

Comprehensive resource for the scientific community working with Arabidopsis thaliana.

links directory index: 503
TitlePublication YearGoogle Scholar Citation Count
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community2003503
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tagsarabidopsis arabidopsis proteins biological models genetic databases genetic polymorphism oligonucleotide array sequence analysis plant genome

WhETSTool Content

http://www.rothamsted.ac.uk/whets/ [open in a new window]

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DNA > Sequence Polymorphisms
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching and Classification

WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.

This content is being maintained by RowanMitchell.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence200710
NAR Web Server Issue 2007
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tagscomputational biology expressed sequence tags genetic databases genetic models plant chromosomes plant genes plant genome ploidies sequence alignment single nucleotide polymorphism triticum

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