iTerm-PseKNC 2.0 – Identifying Terminator

iTerm-PseKNC 2.0

:: DESCRIPTION

iTerm-PseKNC is a webserver for the identification of bacterial transcriptional terminators based on machine learning method.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser / Linux

:: DOWNLOAD

iTerm-PseKNC

:: MORE INFORMATION

Citation

iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators.
Feng CQ, Zhang ZY, Zhu XJ, Lin Y, Chen W, Tang H, Lin H.
Bioinformatics. 2019 May 1;35(9):1469-1477. doi: 10.1093/bioinformatics/bty827.

GeSTer – Dentify Terminators in Bacterial Genome Sequences

GeSTer

:: DESCRIPTION

GeSTer (GenomeScanner for Terminators) softwre first segregates the coding, upstream, and downstream regions based on the feature table entries of the genome sequence. Next it searches for palindromic sequences downstream of each gene (?20 to +270 nucleotides of the stop codon) without entering adjacent coding regions. The search is initiated at a G/C-rich (>50%) tetranucleotide, and a reverse complementary match is sought within the next 70 nucleotides. This defines the base of the stem, and the match is extended inward. Once a mismatch is encountered, all possible structures are computed allowing for different combinations of mismatches and gaps. The ΔGof formation of each of these structures was computed using the parameters from Turner et al. (22) and Jaeger et al. (23). Among all these structures, the one with the lowest ΔG was retained. Then the program moved to the next G/C-rich tetranucleotide and reinitiated the search.

::DEVELOPER

Ranjana Prakash,Indian Institute of Science, Bangalore. India

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GeSTer

:: MORE INFORMATION

Citation

Unniraman S, Prakash R, Nagaraja V:
Alternate paradigm for intrinsic transcription termination in eubacteria.
J Biol Chem 2001, 276:41850-55.

TransTermHP 2.09 – Transcription Terminator Predictions

TransTermHP 2.09

:: DESCRIPTION

TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TransTermHP

:: MORE INFORMATION

Citation:

C. Kingsford, K. Ayanbule and S.L. Salzberg.
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.
Genome Biology 8:R22 (2007).