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DNA/RNA Sequence Homology&Structure Analyses

2010-04-19 21:32:57| 分类：生信分析软件 | 标签： |举报 |字号大中小订阅

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DNA/RNA Sequence HomologyStructure Analyses - fhqdddddd - 流浪云南

Index of Resources

DNA Sequence Homology Analysis and Searching

DNA/RNA Structure & Function Analyses

Multifunction Search & Data Retrieval Searchers

Nucleotide Sequence Alignment Servers

Sequence Manipulation Tools

Miscellaneous Analyses

BLAST - Basic Local Alignment Search Tool - NCBI (US)

BLAST - GeneStream - IGH Montpellier (France)
BLAST - GenomeNet (Japan)
BLAST - DDBJ (Japan)
BLAST - DISC/AFFRC (Japan)
BLAST - Compugen (US/Israel)
BLAST - ORNL (US)
BLAST - Stanford U (US)
BLAST - NCBI (US)
BLAST - BCM (US)
THC-Blast - Tentative Human Consensus Sequences BLAST - NCBI (US)

BLAST2 - Gapped BLAST - NCBI (US)

BLAST2 - Pasteur Institute (France)
BLAST2 - EMBL (Germany)
COMPBLAST - TigemNet (Italy)
BLAST2 - ExPasy (Switzerland)
BLAST2 - Compugen (US/Israel)
BLAST2 - NCBI (US)

Est Extractor - BLAST search against dbEST - TigemNet (Italy)

FASTA - Pearson and Lipman(Algorithm)Sequence Comparison Service

FASTA - GeneStream - IGH Montpellier (France)
FASTA - Weisman Institute (Israel)
FASTA - DDBJ (Japan)
FASTA - DISC/AFFRC (Japan)
FASTA - EBI (UK)
FASTA - ORNL (US)
FASTA - Stanford U (US)

GenLang - Linguistic Sequence Analyzer - CBIL (US)

GenQuest - Query Nucleotide/Protein Sequence Comparison against Nucleotide/Protein Sequence Databases - ORNL (US)

PHI-BLAST - Pattern Hit Initiated BLAST - NCBI (US)

Plant Expressed Sequence Tags Analysis - Sequence Identity Comparison to the Plant cDNA/EST Database - U Minnesota (US)

ProfileScan - Sequence Homology Search using a Profiles Library - ISREC (Switzerland)

PSI-BLAST - Position Specific Iterated BLAST - NCBI (US)

SW DNA Search - AFFRC (Japan)

UNIBLAST - BLAST against organism specific subset of GenBank - TigemNet (Italy)

Zinfo - Nucleotide Sequence Analysis for Regions of Atypical Genomic Organization - VGC (US)

Protein Search Using A Nucleotide Sequence

MPsrch-NTP/NTPA - DISC/AFFRC (Japan)
NuclPepSearch - Searching SwissProt for a nucleotide sequence - ETHZ (Switzerland)

Gene Search Using A Protein Sequence

MPsrch-TPN/TPNA - DISC/AFFRC (Japan)

FASTPAT - FASTA-based Patterns Database Search at the - BCM (US)

GenLang - Gene Structure & Transcriptional Element Features Prediction - U Pennsylvania (US)

MEME - Multiple EM for Motif Elicitation

MEME - Pasteur Institute (France)
MEME - SDSC (US)

PatScan - DNA Sequence Motif Analysis - ANL (US)

Poly-A Site Prediction

HCpolyA - Poly-A Site Prediction (Hamming Clustering Method) - WebGene Server (Italy)
POLYA - Recognition of 3'-end Cleavage & Poly-A Signals - BCM (US)

Exon (ORF) Prediction

Cassandra - Recognition of Protein-Coding Segments - CCEG-USC (US)
CDSB - Search for Protein Coding Regions in E.coli - BCM (US)
DNA Sequence Translation - Analysis of ORF in Gene Sequence - U Minnesota (US)
FramePlot - Protein Coding Region Prediction in Bacterial DNA - NIH-NET (Japan)
Gene Finder - Gene Structural Analysis, Exon and Splice Site Prediction - BCM (US)
GENEID - Prediction of Exons and Gene Structure in Query Sequences (US)
GenHunt - Search for Exons in Query Sequence - Weisman Institute (Israel)
GENIE - Gene (Prediction) Finder
- GENIE - Gene [prediction] Finder - LBNL Human Genome Center (US)
- Genie - BCM (US)
GenView - Protein-Coding Gene Prediction - WebGene Server (Italy)
GRAIL - Exon Prediction/Analysis
- GRAIL - ORNL (US)
- GRAIL - ORNL (US)
- GRAIL - BCM (US)
HEXON - Search for Prediction of Internal Exons in Human DNA - BCM (US)
ORD ID - Open Reading Frame Identification - UMMC (US)
ORF Finder - Open Reading Frame Finder at - NCBI (US)
ORFGene - Gene Structure Prediction - WebGene Server (Italy)
Prediction of Gene Structure in DNA Sequence from
- Drosophila [FGENED] - BCM (US)
- Human [FGENEH] - BCM (US)
- Nematode [FGENEN] - BCM (US)
- Plant [FGENEA] - BCM (US)
Prediction of Potential 5'-,Internal, & 3'-Exons in DNA sequence from
- Drosophila [FEXD] - BCM (US)
- Human [FEXH] - BCM (US)
- Nematode [FEXN] - BCM (US)
- Plant [FEXA] - BCM (US)
- Yeast [FEXY] - BCM (US)
PROCRUSTES - Gene Recognition via Spliced Alignment - USC (US)

Splice Site Prediction

Gene Finder - Gene Structural Analysis, Exon and Splice Site Prediction - BCM (US)
NetGene - Splice Site Location Prediction Email-Server Information (US)
NNSSP - Splice Site Prediction by Neural Network - LBNL Human Genome Center (US)
Search/Prediction of Potential Splice Sites in DNA
- Drosophila [DSPL] (BCM Gene Finder) - BCM (US)
- Human [HSPL] (BCM Gene Finder) - BCM (US)
- Nematode [NSPL] (BCM Gene Finder) - BCM (US)
- Plants [ASPL] (BCM Gene Finder) - BCM (US)
- Yeast [RNASPL] (BCM Gene Finder) - BCM (US)
Splice Site - Splice Site Prediction by Neural Network - LBNL (US)
SpliceView - Splicing Signals Prediction - WebGene Server (Italy)
YSPL (BCM Gene Finder) - Search for Exon-Exon Junction Positions in cDNA - BCM (US)

TATA Signaling, Promoter & Trans-Factor Bind Site Prediction

HCtata - TATA Signaling Prediction (Hamming Clustering Method) - WebGene Server (Italy)
MatInspector - Search Sequence for Transcription Factor Binding Sites - GSF (Germany)
McPromoter - Prediction of Transcription Start Sites in Eukaryotic DNA - Univ Erlangen (Germany)
NNPP - Promoter Prediction - LBNL Human Genome Center (US)
Recognition of PolII Promoter Region & Transcription Start Signals Using
- TSSG (BCM Gene Finder) - promoter.dat TFD Subset - BCM (US)
- TSSW (BCM Gene Finder) - TRANSFAC Database - BCM (US)
Signal Scan - Search Search for Eukaryotic Transcriptional Elements - BIMAS (US)
Target Finder - Search for target genes of DNA-binding proteins - TigemNet (Italy)
TESS - Transcription Factor Binding Site Sequence Search - U Penn (US)
Tfsitescan - Promoter analysis - MIRAGE -IFTI (US)

Repetitive DNA & CpG Isles Analyses

CENSOR - Query Sequence Comparison against Human/Rodent Repeats Database - GIRI (US)
GRAIL - CpG Isle, Repetitive DNA prediction/Analysis
- GRAIL - ORNL (US)
- GRAIL - BCM (US)
PYTHIA - Identification of Human Repetitive DNA (US)
RepEater - Search for Sequence Repeats in Query Sequence - Weisman Institute (Israel)
RepeatMasker2 - Analysis of Repetitive Elements in DNA Sequences - U Washington (US)

tRNA Gene Prediction

Pol3Scan - Analysis of tRNA Genes & Related Elements - ISB (Italy)
tRNAscan - Genomic tRNA Gene Identification - WUSTL (US)

ENTREZ - Nucleotide Sequench Search - NCBI (US)

BEAUTY - BLAST Enhanced Alignment Utility - BCM (US)

Clustal-W, MAP, & PIMA Multiple Sequence Alignments - BCM (US)

ClustalW 1.6 - Global Progressive Sequence Alignments - BCM (US)

DOT PLOT - Self DNA Comparison - VGC (US)

LALIGN - Calculates N-Best Local Alignments between Two Sequences - GeneStream - IGH Montpellier (France)

LFASTA - Local Similarity Search between Two Sequences (Local Alignments Displayed) - GeneStream - IGH Montpellier (France)

MAP - Multiple Sequence Alignments - BCM (US)

MSA - Multiple Sequence Alignments - IBC-WUSTL (US)

Sequence-To-Cluster - Align Query Sequence aginst PIMA Multiple Alignment/Pattern - BCM (US)

CAP EST Assembler - Contig Assembly Program Fragment Assembler - IFOM (Italy)

EULER - EULER Fragment Assembler - SDSC (US)

Sequence Orientation Conversion Utilities

ReadSeq - Sequence Format Conversion Utility - BCM (US)
Reverse Complement - Sequence Orientation Conversion Tool - BCM (US)
Reverse, Complement or Reverse and Complement - Sequence Orientation Conversion Tool - EMBL-Heidelberg (Germany)

Restriction Enzyme Mapping Analysis

RE Finder - Roche Molecular Biochemicals (US)
tacg V3 - Restriction Enzyme Analysis & Mapping
WebCutter - Restriction Mapping Tool
- WebCutter - Goteborgs U (Sweden)
- WebCutter - First Market (USA)
WebGene - Restriction Enzyme Cleavage Analysis - SUNY-Geneseo (US)

Translate a DNA Sequence into a Protein

6 Frame Translation Tool - Translate DNA Sequence in all 6 Frames - BCM (US)
DNA Sequence Translation - U Minnesota Medical School (US)
The Protein Machine - Protein Translation - EBI (UK)
Translate Tool - Protein Translation - ExPasy (Switzerland)

Sequence Presentation/Publication Tools

BOXSHADE - Printing and Shading of Multiple Sequence Alignments - ISREC (Switzerland)

Chimera Server - Determine if 16S rRNA Sequence is Chimeric - CCEG-USC (US)

HRB (BCM Gene Finder) - Recognition of Human & E. coli Sequences to Test a Library for E. coli Contamination - BCM (US)

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