Genome Annotation
Software name Description FTG A web server for locating probable protein coding region in nucleotide sequence using fourier tranform approach. GWBLAST A 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. GWFASTA Genome 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. EGPred This 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. SVMgene It is a support vector based approach to identify the protein coding regions in human genomic DNA. SRF Spectral 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. MyPattern MyPattern 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)). GeneBench A suite of datasets and tools for evaluating gene prediction methods. FTGPred A web server for predicting genes in a DNAsequence. PHDcleav Prediction of Human Dicer cleavage. PolyApred PolyApred is a support vector machine (SVM) based method for the prediction of polyadenylation signal (PAS) in human DNA sequence. siRNAPred Support vector machine based methods for predicting actual efficacy of both 21mer and 19mer siRNAs with high accuracy. ECGPred This 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. SGpred This server allows user to identify and visulaze the genes which have different expression level in normal and disease conditions. desiRam A support vector machine model for predicting siRNA efficacy on existing datasets. MARSpred A prediction method MARSpred for discrimination between Mitochondrial-AARSs and Cytosolic-AARSs. Icaars Identification & Classification of Aminoacyl tRNA Synthetases. Blast+ BLAST finds regions of local similarity between sequences blast2go Blast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Bowtie Bowtie is ab ultrafast memory-efficient short read aligner. Boxshade This 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. BWA BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. CD-HIT Programs designed to quickly align and group sequences. CIRCOS Circos creates data visualization with a circular layout. Clustalx ClustalX: This version has a graphical user interface for clustax. Cufflinks Transcript assembly, differential expression and regulation for RNA-Seq EMBOSS complete European 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. IGV Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations. JMol Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. MEME/MAST Search for common motifs in DNA or protein sequences. MIRA Whole Genome Shotgun and EST Sequence Assembler MUMMER MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. MUSCLE MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. It is much better and fast algorithm for sequence alignment. njplot Phylogenetic tree drawing program. PHYLIP NEW-3.67 Package of programs for inferring phylogenies. primer3 Tool to design flanking oligo nucleotides for DNA amplification. RasMol Randomized Axelerated Maximum Likelihood of phylogenetic trees. Readseq Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Samtools Processing sequence alignments in SAM and BAM formats. SOAPdenovo SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. SVM_Light SVMLight is an implementation of Support Vector Machine (SVM) in C developed for the purpose of machine learning. Velvet Nucleic acid sequence assembler for very short reads, long version.
Software name Description FTG A web server for locating probable protein coding region in nucleotide sequence using fourier tranform approach. GWBLAST A 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. GWFASTA Genome 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. EGPred This 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. SVMgene It is a support vector based approach to identify the protein coding regions in human genomic DNA. SRF Spectral 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. MyPattern MyPattern 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)). GeneBench A suite of datasets and tools for evaluating gene prediction methods. FTGPred A web server for predicting genes in a DNAsequence. PHDcleav Prediction of Human Dicer cleavage. PolyApred PolyApred is a support vector machine (SVM) based method for the prediction of polyadenylation signal (PAS) in human DNA sequence. siRNAPred Support vector machine based methods for predicting actual efficacy of both 21mer and 19mer siRNAs with high accuracy. ECGPred This 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. SGpred This server allows user to identify and visulaze the genes which have different expression level in normal and disease conditions. desiRam A support vector machine model for predicting siRNA efficacy on existing datasets. MARSpred A prediction method MARSpred for discrimination between Mitochondrial-AARSs and Cytosolic-AARSs. Icaars Identification & Classification of Aminoacyl tRNA Synthetases.
Software name Usage icaars Usage: 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
MARSpred Usage: MARSpred.php inputfile tool(1/2) method(1/2/3) threshold outputfile RNAcon Usage: ./rnacon.pl -i input_RNA_fasta_file -t threshold -o output_file Genomeabc A web server for evaluating the performance of genome assemblers
Software name Description Desirm Designing 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 Icaars Identification & classification of aminoacyl-tRNA synthetases
Software name Description Clustalx ClustalX: This version has a graphical user interface for clustax. Jalview A Java multiple sequence alignment editor Ugene Free cross-platform bioinformatics software package for DNA and protein sequence analysis.
Software name Description Bowtie Bowtie is ab ultrafast memory-efficient short read aligner. BWA BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. CD-HIT Programs designed to quickly align and group sequences. CIRCOS Circos creates data visualization with a circular layout. Clustalx ClustalX: This version has a graphical user interface for clustax. Cufflinks Transcript assembly, differential expression and regulation for RNA-Seq EMBOSS complete European 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. IGV Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations. JMol Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. MEME/MAST Search for common motifs in DNA or protein sequences. MUMMER MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. njplot Phylogenetic tree drawing program. PHYLIP Package of programs for inferring phylogenies. primer3 Tool to design flanking oligo nucleotides for DNA amplification. RasMol Randomized Axelerated Maximum Likelihood of phylogenetic trees. Readseq Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Samtools Processing sequence alignments in SAM and BAM formats. Velvet Nucleic acid sequence assembler for very short reads, long version.