pairwise alignment

The ProteinALIGNment (Palign) programs are a set of programs for sequence searches. They can perform standard dynamic programming, heuristic fasta like searches and profile-profile alignments. Palign can be used for many type of alignment problems and can:

1. Align two sequences and search a database with a sequence
2. Align a sequence and a profile
3. Include and combine secondary structure information into the alignments
4. Read sequences, profiles etc in many formats
5. Perform profile-profile searches/alignments using different algorithms

SHRIMP

tBLASTx finds regions of similarity between the six-frame translations of a nucleotide query sequence and the six-frame translations of a nucleotide sequence database.
Computations are done on the Vital-IT cluster (SIB).
Most NCBI BLAST (2.2.17) options are available.
Most SIB databases are available: STS, EST, HTG, refseq, repbase, ...

INPUT: nucleotide sequence(s) + choose a database
OUTPUT: BLAST output

tBLASTn finds regions of similarity between a protein query sequence and a nucleotide sequence database dynamically translated in all reading frames.
Computations are done on the Vital-IT cluster (SIB).
Most NCBI BLAST (2.2.17) options are available.
Most SIB databases are available: Uniprot, UniRef, organism proteomes, refseq protein, nrl3D, ...

INPUT: protein sequence(s) + choose a database
OUTPUT: BLAST output

psiBLAST finds regions of low similarity between peptides (Position-Specific Iterated BLAST).
Computations are done on the Vital-IT cluster (SIB).
Most NCBI BLAST (2.2.17) options are available.
Most SIB databases are available: Uniprot, UniRef, organism proteomes, refseq protein, nrl3D, ...

INPUT: protein sequence(s) + choose a database
OUTPUT: BLAST output