ISSH – Iterative Spaced Seed Hashing

ISSH

:: DESCRIPTION

ISSH is an iterative algorithm that combines multiple spaced seed hashes by exploiting the similarity of adjacent hash values in order to efficiently compute the next hash.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ISSH

:: MORE INFORMATION

Citation

E.Petrucci, L.Noé, C. Pizzi, M. Comin
Iterative Spaced Seed Hashing: Closing the gap between spaced seed hashing and k-mer hashing
In Proceedings of the 15th International Symposium on Bioinformatics Research and Applications, pp. 208-219.

FISH – Fast Indexing for Spaced-seed Hashing

FISH

:: DESCRIPTION

FISH is a novel algorithm,which based on the indexing of small blocks that can be combined to obtain the hashing of spaced-seeds of any length. The method exploits the fast computation of the hashing of runs of consecutive 1 in the spaced seeds, that basically correspond to k-mer of the length of the run.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

FISH

:: MORE INFORMATION

Citation

BMC Bioinformatics, 19 (Suppl 15), 441 2018 Nov 30
Efficient Computation of Spaced Seed Hashing With Block Indexing
Samuele Girotto , Matteo Comin , Cinzia Pizzi

SpEED – Fast Computation of Sensitive Spaced Seeds

SpEED

:: DESCRIPTION

SpEED is a software program that computes highly sensitive multiple spaced seeds.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SpEED

:: MORE INFORMATION

Citation

SpEED: fast computation of sensitive spaced seeds.
Ilie L, Ilie S, Bigvand AM.
Bioinformatics. 2011 Sep 1;27(17):2433-4. doi: 10.1093/bioinformatics/btr368.