ProbeAlign 0.3 – ncRNA Homology Search

ProbeAlign 0.3

:: DESCRIPTION

ProbeAlign is a program for annotating ncRNA structures by incorporating high-throughput sequencing based structure probing information.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ProbeAlign

:: MORE INFORMATION

Citation:

ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.
Ge P, Zhong C, Zhang S.
BMC Bioinformatics. 2014;15 Suppl 9:S15. doi: 10.1186/1471-2105-15-S9-S15.

GHOSTZ 1.0.2 / GHOSTZ-GPU 1.1.0 – Homology Search tool

GHOSTZ 1.0.2 / GHOSTZ-GPU 1.1.0

:: DESCRIPTION

GHOSTZ is a homology search tool which can detect remote homologues like BLAST and is about 200 times more efficient than BLAST by using database subsequence clustering. GHOSTZ outputs search results in the format similar to BLAST-tabular format.

GHOSTZ-GPU is a homology search tool which can detect remote homologues like BLAST and is about 5-7 times more efficient than GHOSTZ by using GHOSTZ-GPU. GHOSTZ-GPU outputs search results in the format similar to BLAST-tabular format.

::DEVELOPER

Akiyama Laboratory , Tokyo Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 GHOSTZ / GHOSTZ-GPU

:: MORE INFORMATION

Citation

Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama.
GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering,
PLoS ONE 11(8): e0157338, 2016. doi: 10.1371/journal.pone.0157338

Faster sequence homology searches by clustering subsequences.
Suzuki S, Kakuta M, Ishida T, Akiyama Y.
Bioinformatics. 2014 Nov 27. pii: btu780.

GHOSTX 1.3.7 – Homology Search tool

GHOSTX 1.3.7

:: DESCRIPTION

GHOSTX is a homology search tool which can detect remote homologues like BLAST and is about 100 times more efficient than BLAST by using suffix arrays.

::DEVELOPER

Akiyama Laboratory , Tokyo Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 GHOSTX

:: MORE INFORMATION

Citation

PLoS One. 2014 Aug 6;9(8):e103833. doi: 10.1371/journal.pone.0103833. eCollection 2014.
GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array.
Suzuki S, Kakuta M, Ishida T, Akiyama Y.

LocARNAscan 1.0 – Homology Search for Structured RNAs

LocARNAscan 1.0

:: DESCRIPTION

LocARNAscan is a semi-global scanning variant of LocARNA’s algorithm for sequence-structure alignment.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 LocARNAscan

:: MORE INFORMATION

Citation:

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.
Will S, Siebauer MF, Heyne S, Engelhardt J, Stadler PF, Reiche, Backofen R.
Algorithms Mol Biol. 2013 Apr 20;8:14. doi: 10.1186/1748-7188-8-14. eCollection 2013.