DNA > Analysis   THE SMALL BIOINFORMATICIAN [PDF file, human molecular genetics rerefence data table]
  • REVIEW: Practical Database Searching   |   Bioinformatics.Org   |   ISCB   |   Pacific Symposia
  • Intro: Pedestrian guide to analysing sequence databases, by Rost and Schneider, 1999
  • Intro: USER'S GUIDE TO THE HUMAN GENOME - The NCBI Handbook
  • Intro: A Science Primer - at NCBI | Current Topics in Genetics Analysis at NIH VideoCasting
  • Courses: Corso di Bioinformatica (Ita) - Bioinformatics Tutorials & Articles
  • Comments: Mining for Bioinformatics Jobs
  • Sequence Analysis Similarity - Align - Pattern - Express - Phylogen - Util - Protein

    *NCBI (newsletter) - Entrez *HGMP-MRC | *UCSC bestlinks *EBI | *Ensembl Server | *EMBL Harvester
    *BCM Search Launcher *Molecular Biology Resources *Pole Lyonnais   |   *TIGEM   |   *TIGR
    *bioinformatik.de | BioWWW  | BioWareDB *Genetic code with aa type *Bioinformatics index | Courses

    1) Initial similarity search

    BLAST  *BLAST at NCBI: Blast 2 Sequences - Blast Genome | Blast vs. your database | MuSeqBox |
           *BLASTN [Mega| Short] - BLASTP [PSI-PHI | Short] - BLASTX - TBLASTN - TBLASTX
           *BLAST at HGMP, EMBL, EBI           *BLAST Traces   |   BLAST2SRS - (Bimpikis et al., 2003)
           *Ensembl BlastSearch (BlastView)
           *Other Similarity Search Sites      *DNA & Protein Analysis at RUCS
           *DNA Sequence Homology Analysis     (from: CMS Molecular Biology Resources)
           *The Sanger Centre: Software        *Software at TIGR   |   Software at CBI
           *Hits alignment: MView (at Pasteur) *WebBallastpostprocessing
           *MacBOB parser | Blast Parser       *MedBlast: articles about a sequence
           *OntoBlast     | Soap-HT-BLAST: high throughput BLAST (Wang and Mu, 2003)
           *Oracle Database 10g - BLAST search and Regular Expression pattern matching (Stephens et al., 2005)
    Gene prediction/ gene features search:
    Genome annotation

    2) Alignment of Hits Similarity - Pattern - Express - Phylogen - Util - Protein

    Pairwise Sequence comparison

    Next Generation Sequencing - Alignment

  • Documents/Guides
  • Wiki List of Sequence Alignment Software
  • GEM Mapper
  • Multiple Sequence Alignments

    MUTATION EFFECT
  • PredictSNP - predictions of missense mutation effects
  • DDIG-in - probability of disease
  • NNSPLICE - estimation of splice site strength
  • GeneHub-GEPIS (Gene Expression Profiling In Silico) - gene expression patterns from integrated EST and tissue source information
  • 5'SAGE - 5'-end Serial Analysis of Gene Expression database (Kasai et al., 2005)
  • SAGE Gene to Tag Mapping
  • MIRAGE (Molecular Informatics Resource for the Analysis of Gene Expression)
  • DNA ARRAYS (in our "Methods" section)
  •             Phenotype