Tag: Structural Alignment

STAMP 4.4.2 – Structural Alignment of Multiple Proteins

STAMP 4.4.2

:: DESCRIPTION

STAMP is a package for the alignment of protein sequences based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit’ superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. If you are after a multiple sequence alignment for proteins of unknown 3D structure, stop reading now and contact GJB for information about AMPS, which can be used to perform multiple sequence alignments, or see www.jalview.org for GJB’s latest methods for this problem.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window with Cygwin
  • GCC

:: DOWNLOAD

STAMP

:: MORE INFORMATION

Citation

Proteins. 1992 Oct;14(2):309-23.
Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.
Russell RB1, Barton GJ.

SeSAW 2.0 – Functional Mapping by Sequence-Derived Structural Alignment Weights

SeSAW 2.0

:: DESCRIPTION

SeSAW (sequence-derived structural alignment weights) is a web-based program for identifying functionally or evolutionarily conserved motifs in protein structures by locating sequence and structural similarities, and quantifying these at the level of individual residues. Results can be visualized in 2D, as annotated alignments, or in 3D, as structural superpositions. An example is given for both an experimentally determined query structure and a homology model.

::DEVELOPER

Department of Genome Informatics; Research Institute for Microbial Diseases; Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

SeSAW: balancing sequence and structural information in protein functional mapping.
Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H.
Bioinformatics. 2010 May 1;26(9):1258-9. Epub 2010 Mar 17.

DIAL – 3-Dimensional RNA Structural Alignment and Motif Detection

DIAL

:: DESCRIPTION

DIAL is a web server for 3-dimensional RNA structural alignment (global and local) and for motif detection. DIAL (DIhedral ALignment) runs in time that is quadratic in input length by performing an alignment which accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity, (iii) nucleotide base-pairing similarity.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

DIAL

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

F. Ferre; Y. Ponty; W. A. Lorenz; Peter Clote
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities ,
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W659-68. Epub 2007 Jun 13.

SARA-Coffee 1.0.7 – Accurate Multiple RNA Structural Alignment

SARA-Coffee 1.0.7

:: DESCRIPTION

SARA-Coffee is a structure based multiple RNA aligner. This is a new algorithm that joins the pairwise RNA structure alignments performed by SARA with the multiple sequence T-Coffee framework. SARA-Coffee is part of the T-Coffee distribution.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SARA-Coffee

:: MORE INFORMATION

Citation:

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.
Di Tommaso P, Bussotti G, Kemena C, Capriotti E, Chatzou M, Prieto P, Notredame C.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60. doi: 10.1093/nar/gku459.

RNApasta 1.6 – RNA Structural Alignment & Statistical Analysis

RNApasta 1.6

:: DESCRIPTION

RNApasta is a utility for collecting statistics from aligned and structurally annotated RNA sequences.RNApasta is a java utility intended to work with RNA structural alignments, including the motifs of stem-loops and pseudoknots.  RNApasta can perform a variety of statistical analyses, and has editing capabilities intended to be useful with alignments that contain variable data such as the presence or absence of stem-loops or pseudoknots across sequences.  RNApasta can read Rfam-stockholm formatted files or pasta formatted files.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNApasta

:: MORE INFORMATION

Citation

Malmberg, R., Shaw, T., and Cai, L. (2010)
RNApasta: a tool for analysis of RNA structural alignments,
Int J Bioinform Res Appl. 2010;6(6):571-83.

SSU-ALIGN 0.1.1 – Structural Alignment of SSU rRNA Sequences

SSU-ALIGN 0.1.1

:: DESCRIPTION

SSU-ALIGN is a tool for aligning, masking and visualizing archael 16S, bacterial 16S and eukaryotic 18S small subunit ribosomal RNA (SSU rRNA) sequences.

::DEVELOPER

Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SSU-ALIGN

:: MORE INFORMATION

Citation

Structural RNA Homology Search and Alignment Using Covariance Models.
E. P. Nawrocki.
PhD Thesis: Washington University School of Medicine, 2009.

PCSHMM 1.1 – Structural Alignment of RNAs using Profile-csHMMs

PCSHMM 1.1

:: DESCRIPTION

PCSHMM (Profile-csHMM, Profile Context-Sensitive HMM) is a software for finding structural alignment of RNAs including pseudoknots based on profile-csHMMs

::DEVELOPER

Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX

:: DOWNLOAD

 PCSHMM

:: MORE INFORMATION

Citation

Structural alignment of RNAs using profile-csHMMs and its application to RNA homology search: Overview and new results
Byung-Jun Yoon and P. P. Vaidyanathan,
IEEE Transactions on Circuits and Systems: Part-I, IEEE Transactions on Automatic Control (Joint Special Issue on Systems Biology), vol. 53, pp. 10-25, Jan. 2008.

Exalign 1.0 – Gene Structural Alignments and Database Search

Exalign 1.0

:: DESCRIPTION

Exalign is a tool that performs alignments of gene exonic structures. In particular it works by aligning arrays representing the exon lengths of genes. While the aligning algorithms used by Exalign are the well known Smith-Waterman and Needleman-Wunsch ones (with a suitable scoring function), the program performs a post-processing step that tries to identify intron gain/loss events (see sections about exon merging).

::DEVELOPER

Bioinformatics Evolution @nd COmparative geNomics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Complier

:: DOWNLOAD

 Exalign

:: MORE INFORMATION

Citation:

Pavesi G, Zambelli F, Caggese C, Pesole G.
Exalign: a new method for comparative analysis of exon-intron gene structures.
Nucleic Acids Res. 2008 May;36(8):e47. Epub 2008 Apr 8.

PicXAA 1.03 / PicXAA-R 1.0 – Probabilistic Maximum Accuracy Alignment / for RNA Structural Alignment

PicXAA 1.03 / PicXAA-R 1.0

:: DESCRIPTION

PicXAA is a probabilistic non-progressive alignment algorithm that finds protein multiple sequence alignments with maximum expected accuracy.

PicXAA-R is an extension of PicXAA for greedy structural alignment of NonCoding RNAs.

::DEVELOPER

Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PicXAA / PicXAA-R 

:: MORE INFORMATION

Citation

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
Nucleic Acids Research, 38(15):4917-4928, 2010.

PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
BMC Bioinformatics, 12(Suppl 1):S38, 2011