Computational Framework for Biotechnological Research

Sequence analysis

Sequence analysis can be used to assign function to genes and proteins by the study of the similarities between the compared sequences, revealing the evolution and genetic diversity of organisms and Function annotation of genes.

Software Name Description
ALIGN This tool is used to compare 2 sequences, have options for both global and local alignment
CENSOR CENSOR is a software tool which screens query sequences against a reference collection of repeats and "censors" (masks) homologous portions with masking symbols, as well
CLUSTALW2 General purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.
CpG Plot / CpGreport The function of the program cpgplot is to plot CpG rich areas, and cpgreport to report all CpG rich regions.
Genewise Aligns two sequences under the assumption that the sequences share a number of colinear blocks of conservation separated by potentially large and varied lengths of DNA in the two sequences.
Kalign A fast and accurate multiple sequence alignment algorithm.
MAFFT Multiple Alignment using Fast Fourier Transform is a high speed multiple sequence alignment program.
MUSCLE MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation, is claimed to achieve both better average accuracy and better speed.
Pepstats/Pepwindow/Pepinfo Program pepinfo detects and displays various useful metrics about a protein sequence. Pepwindow reads in a protein sequence and displays a graph of the classic Kyte & Doolittle hydropathy plot of that protein. Pepstats outputs a report of simple protein sequence information.
PromoterWise The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
SAPS SAPS evaluates by statistical criteria a wide variety of protein sequence properties. Properties considered include compositional biases, clusters and runs of charge and other amino acid types, different kinds and extents of repetitive structures, locally periodic motifs, and anomalous spacings between identical residue types.
T-coffee T-Coffee is a multiple sequence alignment program. It allows to combine results obtained with several alignment methods.
Transeq Transeq translates nucleic acid sequences to the corresponding peptide sequence. It can translate in any of the 3 forward or three reverse sense frames, or in all three forward or reverse frames, or in all six frames.
COBALT COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST.
Genome Workbench NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.
ORF Finder The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.
Primer - BLAST To help users make primers that are specific to the input PCR template. It uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database.
ProSplign ProSplign is a utility for computing the alignment of proteins to genomic nucleotide sequence. This alignment can include eukaryotic splicing.
Splign Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a compartmentization algorithm which identifies possible gene duplications, and a refined alignment algorithm recognizing introns and splice signals.
VecScreen VecScreen is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin.
WU-BLAST WU-BLAST2 stands for Washington University Basic Local Alignment Search Tool Version 2.0. The emphasis of this tool is to find regions of sequence similarity quickly, with minimum loss of sensitivity.
SeWeR SEquence analysis using WEb Resources, is an integrated portal to common web-based services in bioinformatics.
Motif Search Making the search for promoters and inverted repeats.
DNA Translator Sequence translation from DNA to Proteins.
Non coding RNA Gene Finder Search for Non coding RNA Genes.
TransTerm TransTerm searches for ρ-independent terminators in the vicinity of annotated genes.
QRNA QRNA determined from the nature of the substitutions in blastn alignments, whether it could be in homologous sequences is a non- coding RNA ( ncRNA ).
Clustalformatter 5 Sequence Analysis
BioEdit BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP. An intuitive multiple document interface with convenient features makes alignment and manipulation of sequences relatively easy on your desktop computer.
FASTA FASTA (pronounced FAST-AYE) stands for FAST-ALL, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed.
HMMER 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”.
JAligner An open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment using the affine gap penalty model.
JSTRING Java Search for Tandem Repeats IN Genomes, is graphical and interactive implementation of the algorithm STRING.
NCBI BLAST The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
Gene Runner/ Motif Runner Motif based Sequence Analysis
GoCore GoCore is a free bioinformatics tool for protein sequence alignment and analysis. It operates as an Excel add-in, creating additional menu items that perform the bioinformatics analyses and uses Excel's convenient user interface to provide useful visualizations.
MAFFT Multiple Alignment
MAUVE Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
MEME Suite MEME is a tool for discovering motifs in a group of related DNA or protein sequences.
CORAL (CDTree) Aligning Core Conserved Regions, a powerful tool to aid in the classification of protein sequences and investigate their evolutionary relationships.
BlastAlign BlastAlign: a program that uses blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align.
ARB software The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
ACUA ACUA is a Visual Basic based interface for the Insilico codon analysis. This tool provides various unique features like, Nucleotide analysis, statistical codon analysis, Positional nucleotide analysis and interactive analysis of result.
AnnHyb AnnHyb is a tool for working with and managing nucleotide sequences in multiple formats. The features include sequence viewer, sequence editor, sequence annotation, format conversion, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi-alignment viewer, consensus determination.
SOAP2 SOAP has been in evolution from a single alignment tool to a tool package that provides full solution to next generation sequencing data analysis.
ACT (Artemis Comparison Tool) ACT is a DNA sequence comparison viewer written in Java. It is based on the software for Artemis, the genome viewer and annotation tool.