ELM / iELM 1.0 – Investigation of Functional Sites in Protein Sequences with Eukaryotic Linear Motif database

ELM / iELM 1.0

:: DESCRIPTION

The ELM (Eukaryotic Linear Motif) resource provides the biological community with a comprehensive database of known experimentally validated motifs, and an exploratory tool to discover putative linear motifs in user-submitted protein sequences.

The iELM (interactions of Eukaryotic Linear Motif) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs).

::DEVELOPER

Gibson Group

:: SCREENSHOTS

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Holger Dinkel et al.
ELM — the database of eukaryotic linear motifs
Nucl. Acids Res. (2012) 40 (D1): D242-D251.

iELM – a web server to explore short linear motif-mediated interactions.
Weatheritt RJ, Jehl P, Dinkel H, Gibson TJ. (2012).
Nucleic Acids Res. 2012 Jul

SECISaln 1.0 – Create Structure-based Alignments of an extensive dataset of Eukaryotic SECIS Sequences

SECISaln 1.0

:: DESCRIPTION

SECISaln predicts eukaryotic SECIS elements in a sequence and aligns them against a precompiled database of eukaryotic SECIS elements.

::DEVELOPER

RODERIC GUIGO LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

No. Only web service.

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 1;25(5):674-5. Epub 2009 Jan 29.
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.
Chapple CE, Guigó R, Krol A.

EukRep v0.6.6 – Classification of Eukaryotic and Prokaryotic sequences from Metagenomic datasets

EukRep v0.6.6

:: DESCRIPTION

EukRep is a k-mer-based strategy, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential.

::DEVELOPER

Banfield Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

EukRep

:: MORE INFORMATION

Citation

West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF.
Genome-reconstruction for eukaryotes from complex natural microbial communities.
Genome Res. 2018 Apr;28(4):569-580. doi: 10.1101/gr.228429.117. Epub 2018 Mar 1. PMID: 29496730; PMCID: PMC5880246.

dSSpred – Eukaryotic Donor Splice Site Prediction

dSSpred

:: DESCRIPTION

dSSpred is developed for the prediction of donor splice sites in eukaryotic species. It is based on all possible first order di-nucleotide dependencies that exist in the signal region at the exon-intron boundary.

::DEVELOPER

Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 25;15(1):362.
A statistical approach for 5¿ splice site prediction using short sequence motifs and without encoding sequence data.
Meher P, Sahu T, Rao A, Wahi S.

GlimmerHMM 3.0.4 – Eukaryotic Gene Finder based on GHMM

GlimmerHMM 3.0.4

:: DESCRIPTION

GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM’s GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Sun Solaris / Alpha OSF1

:: DOWNLOAD

GlimmerHMM

:: MORE INFORMATION

GlimmerHMM is OSI Certified Open Source Software .

Citation:

Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879.

GWFASTA – FASTA search in Eukaryotic and Microbial Genomes

GWFASTA

:: DESCRIPTION

GWFASTA (Genome Wise Sequence Similarity Search using FASTA) allows user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search

::DEVELOPER

GWFASTA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Issac, B. and Raghava, G. P. S.(2002)
GWFASTA: A server for FASTA search in Eukaryotic and Microbial genomes.
BioTechniques 33(3):548-556.

Malin 20080413 – Analysis of Eukaryotic Gene Structure Evolution

Malin 20080413

:: DESCRIPTION

Malin is a software package for the analysis of eukaryotic gene structure evolution. It provides a graphical user interface for various tasks commonly used to infer the evolution of exon-intron structure in protein-coding orthologs.

::DEVELOPER

Miklós Csűrös.

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Linux /Windows
Java

:: DOWNLOAD

Malin

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 1;24(13):1538-9. doi: 10.1093/bioinformatics/btn226. Epub 2008 May 12.
Malin: maximum likelihood analysis of intron evolution in eukaryotes.
Csurös M.

GeneZilla 1.22 – GHMM Eukaryotic Gene Finder

GeneZilla 1.22

:: DESCRIPTION

GeneZilla (formerly known as TIGRscan) is a state-of-the-art program for computational prediction of protein-coding genes in eukaryotic DNA, and is based on the Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN and GENIE. It is highly reconfigurable and includes software for retraining by the end-user. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models. It utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, CAP sites, and will soon model CpG islands as well.

::DEVELOPER

Bill Majoros, now at Duke University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX

:: DOWNLOAD

GeneZilla

:: MORE INFORMATION

GeneZilla is available for download as OSI Certified Open Source Software under the Artistic License.

Citation:

Majoros W, et al. (2004) TIGRscan and GlimmerHMM: two open-source ab initio eukaryotic gene finders, Bioinformatics 20, 2878-2879.

GeneSplicer – Detecting Splice Sites in Eukaryotic Genomic DNA

GeneSplicer

:: DESCRIPTION

GeneSplicer is a fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice . Training data sets for human and Arabidopsis thaliana are included.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GCC

:: DOWNLOAD

GeneSplicer

:: MORE INFORMATION

The GeneSplicer software is OSI Certified Open Source Software.

Citation:

Pertea , X. Lin , S. L. Salzberg . GeneSplicer : a new computational method for splice site prediction . Nucleic Acids Res . 2001 Mar 1;29(5):1185-90 .