Tools Organized by function
INDEX -
Analysis -
Documentation -
Databases -
Desk Reference -
Software -
Other Sites
(
NIH Access ONLY ----- 
World Access)
Multifunctional Sites with suites of analysis tools.
- NIH GCG-Lite+
- EMBOSS
- EBI Services
- BCM Search Launcher
- NCSA Biology WorkBench
- Text based Query of Sequence Databases
Search Multiple Databases (Genbank,SwissProt,PIR etc.)
- Entrez - Multiple
Database Query at NCBI/NIH
- GCG-Lite - Sequence Lookup
at CIT/NIH
- Sequence Retrieval System
at EBI, UK
Search DNA Sequence Databases
- GenBank
Database and Update Query at NCBI/NIH
Search Protein Sequence Databases
- GCG-Lite+
- Sequence Locator WAIS search of Protein Databases
at CIT/NIH
- SwissProt Searches
at ExPASy, Switzerland.
- PIR Searches at NBRF
Search 3D Structure Databases
- Molecules R US utility
search PDB at CIT/NIH
- PDB Searches
at PDB
- Nucleic Acid Database Search
at NDB,Rutgers
- Sequence Format Conversion Tools
Utilities which convert between several different sequence
formats
- Format conversion via SEQIO Package
at CIT/NIH
- READSEQ Sequence
Conversion at CIT/NIH
- Database Similarity/homology Searches
Integrated interfaces for the comparison of
DNA and Protein sequence to existing DNA and Protein sequence databases and the rapid
retrieval of the full database entries matched.
- Basic Local Alignment Search Tool (BLAST)
at NCBI/NIH
- Parallel Fasta
for Proteins
at CIT/NIH
- Fasta3 Database Searches
at EBI, UK
- Sequence Alignments
Compare two DNA or Protein Sequences
- GCG BestFit/Gap and Dotplot Utilities
at CIT/NIH
- Dot Plot - Compare a DNA Sequence with Itself
at U. Minnesota
Compare Multiple DNA or Protein Sequences
- Clustal W (1.60)
- Multiple sequence alignment at CIT/NIH
- Clustal W
(1.74) - Multiple sequence alignment at CIT/NIH
- Box_Shade Utility - Stylize the output of a multiple sequence alignment at CIT/NIH
- Determine Restriction Enzyme Cut Sites in DNA
- GCG Map/MapSort Programs at CIT/NIH
- Harry Mangalam's TACG2 program at UC, Irvine
- TACG2 program at CIT/NIH
- Search for matches against "pattern databases"
- Search against the
Prosite database at EBI, UK
- GCG Motifs Program
at CIT/NIH
- Promoter Scan
at CIT/NIH
- Signal Scan
at CIT/NIH
- Protein Sequence Analysis Tools
- GCG-Lite - Protein Sequence Analysis
at CIT/NIH
- SAPS -Statistical Analysis of Protein Sequences
at CIT/NIH
- SAPS at EBI, UK.
- pI/Mw -
Compute the Theoretical pI and Molecular Weight of a Protein Sequence at ExPASy, Switzerland
- Pratt - Search for patterns
conserved in a set of protein, at EBI, UK.
sequences.
- Nucleic Acid Sequence Analysis Tools
- GCG-Lite - DNA Sequence Analysis
(includes map,prime,translate, and reverse translate) at CIT/NIH
- Prime3 - pick PCR primers
from nucleotide sequence (Whitehead Institute)
- BCM Gene
Finder
Predict Splice sites, Protein coding exons and Gene model construction
- Codon Usage
Analysis of Different ORFs in a Gene Sequence at U. Minnesota
- ProteinProspector
at UCSF
- Protein Secondary structure prediction
-
nnPredict at UCSF
-
PHD - Predict Protein Secondary Structure at
EMBL-Heidelberg w/search from
Iowa State
- ProDom
- A Protein Domain Database at
INRA centre in Toulouse, France
- Pfam at
Sanger Centre, UK
- BCM Protein Secondary Structure Prediction
Disclaimer
INDEX -
Analysis -
Documention -
Databases -
Desk Reference -
Software -
Other Sites
Maintained by the
High Performance Scientific Computing Section,
Center for Information Technology
National Institutes of Health