Tag: Non-coding

Sigma 2.0 BETA – Non-coding DNA Sequence Alignment

Sigma 2.0 BETA

:: DESCRIPTION

Sigma (Simple greedy multiple alignment) is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence.This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.

::DEVELOPER

RAHUL SIDDHARTHAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Sigma

:: MORE INFORMATION

Citation:

Rahul Siddharthan,
“Sigma: multiple alignment of weakly-conserved non-coding DNA sequences“,
BMC Bioinformatics 7:143 (2006)

CRISPRDirection 2.0 – Accurate Computational Prediction of Transcribed Strand of CRISPR non-coding RNAs

CRISPRDirection 2.0

:: DESCRIPTION

CRISPRDirection is an algorithm that accurately predicts the strand of the resulting crRNAs.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Java

:: DOWNLOAD

 CRISPRDirection

:: MORE INFORMATION

Citation:

Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs.
Biswas A, Fineran PC, Brown CM.
Bioinformatics. 2014 Jul 1;30(13):1805-13. doi: 10.1093/bioinformatics/btu114.

CNCI v2 – Distinguish Protein-coding and Non-coding Sequences

CNCI v2

:: DESCRIPTION

CNCI (Coding-Non-Coding Index) is a powerful signature tool by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations.

::DEVELOPER

CNCI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CNCI

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Sep;41(17):e166. doi: 10.1093/nar/gkt646. Epub 2013 Jul 27.
Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.
Sun L1, Luo H, Bu D, Zhao G, Yu K, Zhang C, Liu Y, Chen R, Zhao Y.

ncFANs v2 – non-coding RNA Function Annotation Server

ncFANs v2

:: DESCRIPTION

ncFANs (non-coding RNA Function Annotation Server) re-annotates microarray data and predict ncRNAs functions of interest to the user/functions of Your Favorite ncRNA (YFN). The ncFANs services presently includes to two organisms and three microarray platforms. This is the first web service for the function annotation of long ncRNAs. We believe it will be an important tool for researchers to further analyze the roles of long ncRNAs in various biological processes.

::DEVELOPER

Qi Liao, Hui Xiao,Institute of Computing Technology,China

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ncFANs

:: MORE INFORMATION

Citation

ncFANs: a web server for functional annotation of long non-coding RNAs Nucl.
Acids Res. (2011) 39 (suppl 2): W118-W124.
Qi Liao, Hui Xiao, Dechao Bu, Chaoyong Xie, Ruoyu Miao, Haitao Luo, Guoguang Zhao, Kuntao Yu, Haitao Zhao, Geir Skogerb?, Runsheng Chen, Zhongdao Wu, Changning Liu,; Yi Zha

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