Tag: Homology

CopraRNA 2.1.3 – sRNA Target Prediction utilizing Homology

CopraRNA 2.1.3

:: DESCRIPTION

CopraRNA (Comparative Prediction Algorithm for sRNA Targets) is a tool for sRNA target prediction. It computes whole genome predictions by combination of distinct whole genome IntaRNA predictions. As input, CopraRNA requires at least 3 homologous sRNA sequences from 3 distinct organisms in FASTA format.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CopraRNA 

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):E3487-96. doi: 10.1073/pnas.1303248110. Epub 2013 Aug 26.
Comparative genomics boosts target prediction for bacterial small RNAs.
Wright PR1, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J.

Jali 1.3 – Remote Homology Detection for Protein

Jali 1.3

:: DESCRIPTION

Jali (Jumping Alignments) is an alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Watherman algorithm.

::DEVELOPER

Jens Stoye

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Jali

:: MORE INFORMATION

Citation

A novel approach to remote homology detection: Jumping Alignments
R. Spang, M. Rehmsmeier, J. Stoye
J. Comp. Biol., volume 9, pp. 747-760, 2002

CPHmodels 3.2 – Protein Homology Modeling server

CPHmodels 3.2

:: DESCRIPTION

CPHmodels is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Send inquiries by e-mail to software@cbs.dtu.dk.

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W576-81. doi: 10.1093/nar/gkq535. Epub 2010 Jun 11.
CPHmodels-3.0–remote homology modeling using structure-guided sequence profiles.
Nielsen M1, Lundegaard C, Lund O, Petersen TN.

HOMA – Create Homology models of a protein with unknown Structure

HOMA

:: DESCRIPTION

HOMA (Homology Modeling Automatically) is a web-based interface that can create homology models of a protein with unknown structure (the target or query protein) based on a homologous protein with known structure (the template protein).

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web BRowser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2008 Jan 1;70(1):105-18.
Assessing model accuracy using the homology modeling automatically software.
Bhattacharya A, Wunderlich Z, Monleon D, Tejero R, Montelione GT.

MEDELLER – Homology-Based Coordinate Generation for Membrane Proteins

MEDELLER

:: DESCRIPTION

MEDELLER, a MP(Membrane proteins)-specific homology-based coordinate generation method,  which is optimized to build highly reliable core models.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 15;26(22):2833-40. doi: 10.1093/bioinformatics/btq554. Epub 2010 Oct 5.
MEDELLER: homology-based coordinate generation for membrane proteins.
Kelm S, Shi J, Deane CM.

iMembrane – Homology-Based Insertion of Proteins into the Membrane

iMembrane

:: DESCRIPTION

iMembrane is a homology-based method, which predicts a membrane protein’s position within a lipid bilayer. It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
  • Java

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Apr 15;25(8):1086-8. doi: 10.1093/bioinformatics/btp102. Epub 2009 Feb 23.
iMembrane: homology-based membrane-insertion of proteins.
Kelm S, Shi J, Deane CM.

Aequatus – Open-source Homology Browser

Aequatus

:: DESCRIPTION

Aequatus is an open-source web-based tool to visualise homologous gene structures among differing species or subtypes of a common species.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser/ Linux

:: DOWNLOAD

Aequatus

:: MORE INFORMATION

Citation

Aequatus: an open-source homology browser.
Thanki AS, Soranzo N, Herrero J, Haerty W, Davey RP.
Gigascience. 2018 Nov 1;7(11). doi: 10.1093/gigascience/giy128.

PubServer – Literature Searches by Homology

PubServer

:: DESCRIPTION

PubServer collects homologous sequences from NR database and retrieves and filters associated publications.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W430-5. doi: 10.1093/nar/gku450. Epub 2014 Jun 23.
PubServer: literature searches by homology.
Jaroszewski L, Koska L, Sedova M, Godzik A

HMMER 3.2.1 – Protein Sequence Homology Search

HMMER 3.2.1

:: DESCRIPTION

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models Profile Hidden Markov Models for Sequence Analysis.

::DEVELOPER

Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

HMMER

:: MORE INFORMATION

Citation

HMMER web server: 2015 update.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR.
Nucleic Acids Res. 2015 May 5. pii: gkv397.

HMMER web server: interactive sequence similarity searching
R.D. Finn, J. Clements, S.R. Eddy
Nucl. Acids Res. (2011) 39 (suppl 2): W29-W37

R. Durbin, S. Eddy, A. Krogh, and G. Mitchison,
Biological sequence analysis: probabilistic models of proteins and nucleic acids,
Cambridge University Press, 1998.

M-Coffee – Combination of Multiple Sequence Alignment Packages

M-Coffee

:: DESCRIPTION

M-Coffee is a multiple sequence alignment Package. It is part of the T-Coffee distribution. The specificity of M-Coffee is that rather than computing a multiple sequence alignment on its own, it uses other packages to compute the alignments. It then uses T-Coffee to combine all these alignents into one unique final alignment.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Wallace IM, O’Sullivan O, Higgins DG, Notredame C.
Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. Print 2006.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25.