Genome Annotation


jQuery UI Tabs - Default functionality In past large number of software and web servers have been developed for annotating genomes. This page maintain software/severs available at OSDDlinux useful in annotating genome at gene or nucleotide level. In OSDDlinux we have divided these packages in categories i) All for all type ofsoftware, ii) Webservers for web services, iii) Galaxy for software integated in Galaxy, iv) GUI for graphics based software, v) Third for software not belongs to Raghava's group

Software nameDescription
FTGA web server for locating probable protein coding region in nucleotide sequence using fourier tranform approach.
GWBLASTA genome wide blast server. It allow user to search ther sequence against sequenced genomes and annonated proteomes. This integrate various tools which allows analysys of BLAST SEARCH.
GWFASTAGenome Wise Sequence Similarity Search using FASTA. It allow user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search.
EGPredThis server allows to predict gene (protein coding regions) in eukaryote genomes that includes introns and exons, using similarity aided (double) and consensus Ab Intion methods.
SVMgeneIt is a support vector based approach to identify the protein coding regions in human genomic DNA.
SRFSpectral Repeat Finder (SRF) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not.
MyPatternMyPattern Finder is a program for detection of a 'motif' in DNA sequence by using an exact search method (Option A (1.0)) or an alignment technique (Option B (1.0)).
GeneBenchA suite of datasets and tools for evaluating gene prediction methods.
FTGPredA web server for predicting genes in a DNAsequence.
PHDcleavPrediction of Human Dicer cleavage.
PolyApredPolyApred is a support vector machine (SVM) based method for the prediction of polyadenylation signal (PAS) in human DNA sequence.
siRNAPredSupport vector machine based methods for predicting actual efficacy of both 21mer and 19mer siRNAs with high accuracy.
ECGPredThis server allows user to analsis the expresion data (Microarray Data) where it calculate correlation coefficient between level of gene expression and nucleotides composition of genes.
SGpredThis server allows user to identify and visulaze the genes which have different expression level in normal and disease conditions.
desiRamA support vector machine model for predicting siRNA efficacy on existing datasets.
MARSpredA prediction method MARSpred for discrimination between Mitochondrial-AARSs and Cytosolic-AARSs.
IcaarsIdentification & Classification of Aminoacyl tRNA Synthetases.
Blast+BLAST finds regions of local similarity between sequences
blast2goBlast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.
BowtieBowtie is ab ultrafast memory-efficient short read aligner.
BoxshadeThis is a new release of the PASCAL program BOXSHADE , intended for shading multiple aligned sequence files. This is not a completely 'official' release, but makes the new facilities in v3.0 available until Kay can make time to tie up a full release.
BWABWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
CD-HITPrograms designed to quickly align and group sequences.
CIRCOSCircos creates data visualization with a circular layout.
ClustalxClustalX: This version has a graphical user interface for clustax.
CufflinksTranscript assembly, differential expression and regulation for RNA-Seq
EMBOSS completeEuropean molecular biology open software suite. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.
IGVIntegrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations.
JMolOpen source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.
MEME/MASTSearch for common motifs in DNA or protein sequences.
MIRAWhole Genome Shotgun and EST Sequence Assembler
MUMMERMUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
MUSCLEMUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. It is much better and fast algorithm for sequence alignment.
njplotPhylogenetic tree drawing program.
PHYLIP NEW-3.67Package of programs for inferring phylogenies.
primer3Tool to design flanking oligo nucleotides for DNA amplification.
RasMolRandomized Axelerated Maximum Likelihood of phylogenetic trees.
ReadseqConverts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.
SamtoolsProcessing sequence alignments in SAM and BAM formats.
SOAPdenovoSOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.
SVM_LightSVMLight is an implementation of Support Vector Machine (SVM) in C developed for the purpose of machine learning.
VelvetNucleic acid sequence assembler for very short reads, long version.

Software nameDescription
FTGA web server for locating probable protein coding region in nucleotide sequence using fourier tranform approach.
GWBLASTA genome wide blast server. It allow user to search ther sequence against sequenced genomes and annonated proteomes. This integrate various tools which allows analysys of BLAST SEARCH.
GWFASTAGenome Wise Sequence Similarity Search using FASTA. It allow user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search.
EGPredThis server allows to predict gene (protein coding regions) in eukaryote genomes that includes introns and exons, using similarity aided (double) and consensus Ab Intion methods.
SVMgeneIt is a support vector based approach to identify the protein coding regions in human genomic DNA.
SRFSpectral Repeat Finder (SRF) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not.
MyPatternMyPattern Finder is a program for detection of a 'motif' in DNA sequence by using an exact search method (Option A (1.0)) or an alignment technique (Option B (1.0)).
GeneBenchA suite of datasets and tools for evaluating gene prediction methods.
FTGPredA web server for predicting genes in a DNAsequence.
PHDcleavPrediction of Human Dicer cleavage.
PolyApredPolyApred is a support vector machine (SVM) based method for the prediction of polyadenylation signal (PAS) in human DNA sequence.
siRNAPredSupport vector machine based methods for predicting actual efficacy of both 21mer and 19mer siRNAs with high accuracy.
ECGPredThis server allows user to analsis the expresion data (Microarray Data) where it calculate correlation coefficient between level of gene expression and nucleotides composition of genes.
SGpredThis server allows user to identify and visulaze the genes which have different expression level in normal and disease conditions.
desiRamA support vector machine model for predicting siRNA efficacy on existing datasets.
MARSpredA prediction method MARSpred for discrimination between Mitochondrial-AARSs and Cytosolic-AARSs.
IcaarsIdentification & Classification of Aminoacyl tRNA Synthetases.

Software nameUsage
icaarsUsage: perl icaars.pl -i inputfile -m method(1/2/3/4) -r redundancy(1/2/3/4/5/6/7/8) -t threshold -o outputfile
MARSpredUsage: MARSpred.php inputfile tool(1/2) method(1/2/3) threshold outputfile
RNAconUsage: ./rnacon.pl -i input_RNA_fasta_file -t threshold -o output_file
GenomeabcA web server for evaluating the performance of genome assemblers

Software nameDescription
DesirmDesigning of Highly Effective Complementary and Mismatch siRNAs for Silencing a Gene
EGpred Eukaryotic Gene prediction finder
SRF Spectural Repeat finder
PolApred Prediction of polyadenylation signal
Marspred Prediction of mitochondrial aminoacyl-tRNA synthetases
IcaarsIdentification & classification of aminoacyl-tRNA synthetases

Software nameDescription
ClustalxClustalX: This version has a graphical user interface for clustax.
JalviewA Java multiple sequence alignment editor
UgeneFree cross-platform bioinformatics software package for DNA and protein sequence analysis.

Software nameDescription
BowtieBowtie is ab ultrafast memory-efficient short read aligner.
BWABWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
CD-HITPrograms designed to quickly align and group sequences.
CIRCOSCircos creates data visualization with a circular layout.
ClustalxClustalX: This version has a graphical user interface for clustax.
CufflinksTranscript assembly, differential expression and regulation for RNA-Seq
EMBOSS completeEuropean molecular biology open software suite. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.
IGVIntegrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations.
JMolOpen source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.
MEME/MASTSearch for common motifs in DNA or protein sequences.
MUMMERMUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
njplotPhylogenetic tree drawing program.
PHYLIPPackage of programs for inferring phylogenies.
primer3Tool to design flanking oligo nucleotides for DNA amplification.
RasMolRandomized Axelerated Maximum Likelihood of phylogenetic trees.
ReadseqConverts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.
SamtoolsProcessing sequence alignments in SAM and BAM formats.
VelvetNucleic acid sequence assembler for very short reads, long version.