DNA, RNA and Genomic Analysis

Tablet

Tablet Next Generation Sequence Assembly Visualization - is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. File format support for ACE, AFG, MAQ, SOAP2, SAM and BAM. Import GFF3 features and quickly find/highlight/display them. Search and locate reads by name across entire data sets. Entire-contig overviews, showing data layout or coverage information.

BlastStation

BlastStation-Free supports megablast, blastn, blastp, and blastx searches; allows easy database creation from your FASTA or FASTQ file, which can be compressed in .gz, .Z, or .zip format. A graphical display of search results and a summary table display of search results. The latter can be exported in CSV format, while the hit sequences can be exported in FASTA format. Also available for download in Mac or PC format.

DNA 2.0 (Gene Designer)

Gene Designer - a brilliant software tools that allows one to combine building blocks such as regulatory DNA elements (promoters, ribosome-binding sites) with amino acid sequences, affinity & protease cleave tags and cloning features and codon optimize for any expression host.

CLC bio (CLC Free Workbench)

CLC Free Workbench - allows basic sequence analysis such as open reading frame determination, restriction site analysis, translation from DNA/RNA to proteins, alignments, and tree reconstruction in a single window format.

EMBOSS

EMBOSS (European Molecular Biology Open Source Software Suite) can be downloaded from HERE.

PHIRE

PHIRE - this Visual Basic program performs an algorithmic string-based search on bacteriophage genome sequences, discovering and extracting blocks displaying sequence similarity, corresponding to conserved regulatory elements contained within these genomes in a systematic manner, without any prior experimental or predictive knowledge.

Reference: Lavigne, R. et al. 2004. PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics 20: 629-635.

MB DNA Analysis

MB DNA Analysis (Oleg Simakov) - MB is a free multi-functional DNA/protein analysis program. It's main advantage is that it combines all of the most widely used features needed for an advanced molecular analysis of genomic/proteomic data. Features of MB include a fast restriction analysis algorithm (included plasmid / linear DNA drawing), promoter analysis, calculation of molecular weights and chemical properties of proteins, prediction of the secondary protein structures (after Chou-Fasman). Protein analysis also includes sequence translation and codon usage table calculation. Other features: hierarchical multiple sequence alignment tool (with a feature to compare secondary structure of proteins), phylogenetic tree building, dot plot, estimation of isoelectric point for proteins, primer design. A tool for the structural analysis of alpha helices is also included in the main package.

GenePalette

GenePalette allows genome sequence visualization and navigation. Users can download from NCBI's GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.

UGene

UGene (UniPro Bioinformatics Group, Russia) - without a doubt one of the best software packages for genome annotation.

Reference: Okonechnikov K et al. 2012. Bioinformatics 28: 1166-1167.

SEQtools

SEQtools is a program package for routine handling and analysis of DNA and protein sequences. The package includes general facilities for sequence and contig editing, restriction enzyme mapping, translation, and repeat identification. Free for students.

DNA Club

DNA Club - DNA analysis software, features include remove vector sequence, find, find ORF, sequence editing, translate to protein sequence, protein sequence editing, RE Map, RE Map with translation, PCR primer selection, primer or probe evaluation etc.

DNA for Windows

DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects.

RNAdraw

RNAdraw - is an integrated program for RNA secondary structure calculation and analysis by Ole Matzura & Anders Wennborg (1996) Computer Applications in the Biosciences (CABIOS) 12: 247-249.

RNAstructure

RNAstructure - RNA Secondary Structure Prediction and Analysis for Microsoft Windows. This program includes a secondary structure prediction algorithm, a sequence editor, an integrated drawing tool, the OligoWalk program, OligoScreen, Dynalign, and a partition function calculator.

Reference: D.H. Mathews (2005) Bioinformatics 21: 2246 - 2253.

Chromas

Chromas will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create. N.B. only the older versions of the software are free.

FinchTV

FinchTV - Another useful tool for viewing and editing electropherograms.

DNA Master

DNA Master - is "perhaps the world's greatest sequence editor" and analysis package. Find under "computer."

Staden Package

Staden Package - consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin). The package was originally developed at the MRC-LMB in Cambridge. It is now open source (BSD licence) and is hosted on sourceforge.net.

Seqool

Seqool - sequence analysis software designed primarily for searching biological signals in nucleic acid sequences. The sequence analysis program package provides several pattern recognition models, but it also includes the most common sequence analysis statistics, such as GC content, codon usage, etc.

GENtle

GENtle - software package for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.

RepeatAround

RepeatAround - is designed to find "direct repeats", "inverted repeats", "mirror repeats" and "complementary repeats", from 3 bp to 64 bp length, in circular genomes. It processes input files directly extracted from GenBank database or simple sequence. Outputs can be obtained in a spreadsheet containing information on the number and location of the repeats.

Reference: Goios A et al. 2006. Mitochondrion 6: 218-224.

ACUA (Automated Codon Usage Analysis)

ACUA (Automated Codon Usage Analysis; Bioinsilico Technologies) - is a Visual Basic based interface for the Insilico codon analysis. This tool provides various unique features like, Nucleotide analysis, statistical codon analysis. The tool performs Nucleotide analysis for the query sequence(s), and presents the results in spreadsheets, which can be further utilized for statistical analysis. This tool will prove to be highly useful for the scientists who would like to do codon analysis for multiple sequence simultaneously.