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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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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 订阅

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http://mbcf.dfci.harvard.edu/

http://mbcf.dfci.harvard.edu/cmsmbr/

http://mbcf.dfci.harvard.edu/cmsmbr/biotools/biotools16.html

 

 

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)
  • BLAST2 - Gapped BLAST - NCBI (US)
  • Est Extractor - BLAST search against dbEST - TigemNet (Italy)
  • FASTA - Pearson and Lipman(Algorithm)Sequence Comparison Service
  • 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

      Gene Search Using A Protein Sequence

      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
    • 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

        Splice Site Prediction

        TATA Signaling, Promoter & Trans-Factor Bind Site Prediction

        Repetitive DNA & CpG Isles Analyses

        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

              Restriction Enzyme Mapping Analysis

              Translate a DNA Sequence into a Protein

              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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