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UniProt Useful Tools/Links

Various tools and analyses available from the individual UniProt consortium member web sites and other sites that complement the UniProt Databases. These are categorised as Similarity Search, Multiple Sequence Alignment, Batch Retrieval, Proteomics, and Bibliography. There is also a section for Comprehensive Tools/Links Lists.


SIMILARITY SEARCH
Program
Query Type Database Type Description
BLAST (EBI) Sequence Sequence Sequence similarity search
BLAST (PIR) Sequence Sequence Sequence similarity search
BLAST (ExPASy) Sequence Sequence Sequence similarity search
FASTA (EBI) Sequence Sequence Sequence similarity search
FASTA (PIR) Sequence Sequence Sequence similarity search
iProClass (PIR) Sequence Sequence/
Classification
Query a sequence against the iProClass database, which contains both sequences and protein families
InterProScan (EBI) Sequence Domain/
Classification
Query a sequence against the InterPro database, which contains protein families, domains, and motifs
ScanProsite (ExPASy) Sequence/
Pattern
Pattern/
Classification
Scan a protein sequence for patterns, or use a pattern to scan protein sequences
PatMatch (PIR) Sequence/
Pattern/
Peptide
Pattern/
Sequence
Scan a protein sequence for patterns, use a pattern to scan protein sequences, or find exact matches to a peptide
PIRHMM (PIR) Sequence Domain Query a sequence against motif or domain HMMs, or build your own HMM online and query a sequence database

MULTIPLE SEQUENCE ALIGNMENT
Program Alignment Type Description
ClustalW2 (EBI) Multiple Multiple sequence alignment
ClustalW (PIR) Multiple Multiple sequence alignment
SSEARCH (PIR) Pairwise Align two sequences using the Smith-Waterman algorithm
SIM (ExPASy) Pairwise Align two sequences using local similarity

BATCH RETRIEVAL
Title Description
DBFetch (EBI) Retrieve up to 50 entries using IDs/ACs
Batch Retrieval Retrieve up to 10,000 entries using IDs/ACs
Batch Retrieval (ExPASy) Retrieve a list of entries using IDs/ACs


PROTEOMICS
Program Description
Composition/Mw (PIR) Compute amino acid composition and molecular weight based on sequence
Compute pI/Mw (ExPASy) Compute isoelectric point and molecular weight based on sequence
ProtParam (ExPASy) Compute physicochemical parameters based on sequence
ProtScale (ExPASy) Compute hydrophobicity plots and other profiles based on amino acid scales
TagIdent (ExPASy) Identify protein by isoelectric point, molecular weight, or sequence tag
AACompIdent (ExPASy) Identify protein by amino acid composition
Aldente (ExPASy) Identify protein by peptide mass fingerprinting

BIBLIOGRAPHY
Title Description
Medline Search (EBI) Search Medline records

COMPREHENSIVE TOOLS/LINKS LISTS
Links Description
EBI Toolbox Protein analysis tools at EBI
PIR Sequence Analysis Protein analysis tools at PIR
ExPASy Proteomics Protein analysis tools at ExPASy
PIR Links PIR's list of external links
ExPASy links The ExPASy Life Science Directory




















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