RNAmountAlign – RNA Sequence/Structure Alignment

RNAmountAlign

:: DESCRIPTION

RNAmountAlign is a novel algorithm for RNA sequence/structure pairwise alignment, that runs in O(n3) time and O(n2) space; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics as well as parameter fitting.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RNAmountAlign

:: MORE INFORMATION

Citation:

PLoS One, 15 (1), e0227177 2020 Jan 24 eCollection 2020
RNAmountAlign: Efficient Software for Local, Global, Semiglobal Pairwise and Multiple RNA Sequence/Structure Alignment
Amir H Bayegan , Peter Clote

Betascan 20081027 – Predict Beta-sheets from Sequence alone using Pairwise Probabilistic Modeling

Betascan 20081027

:: DESCRIPTION

BETASCAN calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence’s potential beta-structures.

::DEVELOPER

Bonnie Berger , Susan Lindquist , Lenore Cowen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 Betascan

:: MORE INFORMATION

Citation:

BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis.
Bryan AW Jr, Menke M, Cowen LJ, Lindquist SL, Berger B.
PLoS Comput Biol. 2009 Mar;5(3):e1000333. doi: 10.1371/journal.pcbi.1000333.

iMotifs 0.2.5 – Sequence Motif Editor for the Mac

iMotifs 0.2.5

:: DESCRIPTION

iMotifs is a graphical motif analysis environment for the Apple Mac computers (Leopard or later).It allows visualization of annotated sequence motifs and scored motif hits in sequences.

::DEVELOPER

iMotifs team

:: SCREENSHOTS

iMotifs

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

 iMotifs

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Mar 15;26(6):843-4. doi: 10.1093/bioinformatics/btq026. Epub 2010 Jan 26.
iMotifs: an integrated sequence motif visualization and analysis environment.
Piipari M1, Down TA, Saini H, Enright A, Hubbard TJ.

FastMotif – Sequence Motif Discovery

FastMotif

:: DESCRIPTION

FastMotif is a sequence motif discovery algorithm for large DNA datasets, based on spectral methods

::DEVELOPER

FastMotif team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FastMotif

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 16. pii: btv208.
FastMotif: Spectral Sequence Motif Discovery.
Colombo N, Vlassis N

Weeder 2.0 / WeederH 1.0 – Motif Discovery in Sequences from Coregulated Genes of a Single Species

Weeder 2.0 / WeederH 1.0

:: DESCRIPTION

Weeder is an algorithm for the automatic discovery of conserved motifs in a set of related regulatory DNA sequences.

WeederH is a software for finding of conserved nucleotide motifs and regions through comparative genomics, tailored for the analysis of non-coding DNA and the identification of conserved TFBSs or whole enhancers or silencers.

::DEVELOPER

the Research Network of Bioinformatics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Weeder / WeederH

:: MORE INFORMATION

Citation:

Pavesi, G., Mereghetti, P., Mauri, G. and Pesole, G. (2004)
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.
Nucleic Acids Res., 32, W199-203.

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.
Pavesi G, Zambelli F, Pesole G.
BMC Bioinformatics. 2007 Feb 7;8:46.

STAP v2 – Sequence To Affinity Prediction

STAP v2

:: DESCRIPTION

STAP (Sequence To Affinity Prediction) predict transcription factor and DNA interaction affinity and the DNA sequence, considering combinatorial interactions of multiple transcription factors. STAP can be applied to analyze ChIP-seq data.

::DEVELOPER

Zhong Lab / The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GNU Scientific Library (GSL).

:: DOWNLOAD

  STAP

:: MORE INFORMATION

Citation

PLoS One. 2009 Dec 1;4(12):e8155.
A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.
He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

MP-T 201407 – Membrane Protein Sequence-structure Alignment

MP-T 201407

:: DESCRIPTION

MP-T is a sequence-structure alignment algorithm for membrane proteins. It produces accurate sequence alignments for use in homology modelling. The inputs are a fasta-formatted sequence and an annotated structure file from the iMembrane webserver.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MP-T

:: MORE INFORMATION

Citation

Jamie R. Hill and Charlotte M. Deane
MP-T: improving membrane protein alignment for structure prediction
Bioinformatics (2013) 29 (1): 54-61.

ShortCAKE – Shortest sequence to Cover All K-mErs

ShortCAKE

:: DESCRIPTION

ShortCAKE is a software for generating a shortest sequence that for each DNA k-mer includes the k-mer or its reverse complement. In other words, it generates a shortest possible double-stranded sequence covering all k-mers.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  ShortCAKE

:: MORE INFORMATION

Citation

Design of Shortest Double-Stranded DNA Sequences Covering All K-mers with Applications to Protein Binding Microarrays and Synthetic Enhancers,
Yaron Orenstein, Ron Shamir.
Vol. 29 (13), Pages i71-i79, Bioinformatics (2013).doi: 10.1093/bioinformatics/btt230

NYCE – Predict Subcellular Location of Eukaryotic Proteins based on Sequence

NYCE

:: DESCRIPTION

NYCE predicts subcellular location (either Nuclear, Nucleo-cytoplasmic, Cytoplasmic or Extracellular) of eukaryotic proteins using the predicted exposure value of their amino acids.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 28;14:342. doi: 10.1186/1471-2105-14-342.
A novel approach for protein subcellular location prediction using amino acid exposure.
Mer AS1, Andrade-Navarro MA.

CompareProspector – Sequence Motif Finding Algorithm

CompareProspector

:: DESCRIPTION

CompareProspector is a sequence motif-finding algorithm which extends Gibbs sampling by biasing the search in promoter regions conserved across species. Using human–mouse comparison, CompareProspector correctly identified the known motifs for transcription factors Mef2, Myf, Srf, and Sp1 from a set of human muscle-specific genes. It also discovered the NFAT motif from genes upregulated by CD28 stimulation in T cells, which suggests the direct involvement of NFAT in mediating CD28 stimulatory signal. Using C. elegans–C. briggsae comparison, CompareProspector found the PHA-4 motif from pharyngeally expressed genes and the UNC-86 motif from genes known to be regulated by UNC-86. CompareProspector outperformed many other computational motif-finding programs tested, demonstrating the power of comparative genomics-based biased sampling in eukaryotic regulatory element identification.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows with Cygwin / Linux / Mac OsX
  • C Complier

:: DOWNLOAD

 CompareProspector

:: MORE INFORMATION

Citation:

Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S.
Eukaryotic regulatory element conservation analysis and identification using comparative genomics.
Genome Res. 2004 Mar;14(3):451-8.