SsAaTt

sequence search algorithm assessment and testing toolkit (ssaatt)
Harvard Medical site

A complete package for sequence search algorithm comparision


DB dir
Programs dir
PDBG_file dir
Paper dir
Test_set_PARF_files dir

Bio Home
FTP dir 
News
Web sources

Aging
Alignment
Aging/
Alignment/
App@
Artificial_Cell/
Arty@
Artyeast/
BioBean/
BioComponent/
BioEntity/
BioJava/
Bioinformatic_Cell/
Bioinformatics/
Biolux/
Biomatics/
Bioperl/
Biostatistics/
Casp3@
Codon_usage/
DNA/
DNA_chips/
Divclus/
DomainClustering/
Evalign/
FA/
FGAA/
Fasta/
Fetch/
File_formats/
FunGenomics/
Geanfammer/
Gene_finder/
Gene_regulation/
Genechips@
Genome_Analysis
Genomes@
HMM/
HTH/
Homeobox/
Homeodomain@
IMP@
ISL/
ISS/
Life@
Merge_alignments
MoleDynamics/
Olfaction/
PISS/
Pic/
Predator@
Prediction/
Primer_related/
ProD/
ProM/
Protein/
Proteins/
Protenglish/
Proteomics/
Repetitive_seqs/
Rev/
SAGE/
SC_rate
Search_meth_comp
SeqDB_sub_set
Seq_Search/
Sequence_search@
Sequencing/
SimLife/
Simlife@
Smith_waterman/
Str_Genomics/
Structural_Biology/
SymMol/
BioSymmetry
Uasearch/
Utils/
VMD/
Xist
SCOP or FSSP subsets
  • PDB40D-J (935 seq)  Version 1.0
  • PDB40D-J5 (1567 seq) Version 2.0
  • PDB40D-J5.pdbg (PDBG file)
  • NRDB subsets
    1. RSDB90
    2. RSDB80
    3. RSDB70
    4. RSDB60
    5. RSDB50
    6. RSDB40
    7. RSDB30
    8. RSDB20
    Search algorithms
    • simple_psi_blast_search.pl
      • Blastpgp (PSI-Blast)
    Parsers
    • convert_bla_to_msp.pl
    • convert_sso_to_msp.pl
    • write_parf_files.pl
    • write_nhco_files.pl
    Previous Results
     
    Paper
  • The whole paper
  • The peer review
  • reviews
  • response to the reviews
  • Download
    1. The whole package from EBI
      1. from CPAN (perl archive)
    Upload file
    1. to CPAN
    Related sites & machines
    References , FAQs,  Pictures, Utilities and Books etc
    Databases


    WebCrawler ,, InforMine(for Biology data), , Indexed
    MEDLINE, PUBMED, IDEAL, DejaNews , FtpSearch, GOOGLE, Yahoo 
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    jong@salt2.med.harvard.edu