Ssearch with MIQS

Revisiting amino acid substitution matrices for identifying distantly related proteins.
Yamada, K., and Tomii, K. Bioinformatics (2014) 30 (3): 317-325. doi:10.1093/bioinformatics/btt694 [PubMed] [Bioinformatics]

Ssearch in the version 36 of the FASTA program package (see W. R. Pearson and D. J. Lipman (1988), "Improved tools for biological sequence comparison" PNAS 85:2444-2448; W. R. Pearson (1996), "Effective protein sequence comparison" Meth. Enzymol. 266:227-258; and Pearson et. al. (1997), Genomics 46:24-36).

Download benchmark datasets

Substitution matrix

Select a matrix

Query

Amino acid sequence in FASTA format (upto 1000 sequences)Sample sequence


Subject

Amino acid sequence in FASTA format (upto 1000 sequences) Sample sequence 2


Select a database

Ssearch option

:[10,1] E()-value,E()-repeat threshold
:[-10] gap-open penalty
:[-2] gap-extension penalty
on off:filter lowercase (seg) residues
:high scores reported (limited by -E by default)
:number of alignments shown (limited by -E by default)



Now Uploading...
kB / kB