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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. GenePalette allows genome sequence visualization and navigation. A tool for the structural analysis of alpha helices is also included in the main package. 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. Protein analysis also includes sequence translation and codon usage table calculation. 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). 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.

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MB DNA Analysis (Oleg Simakov) - MB is a free multi-functional DNA/protein analysis program. PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. 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.

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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.ĬLC 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.ĮMBOSS ( European Molecular Biology Open Source Software Suite) can be downloaded from here.

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Also available for download in Mac or PC format.

The latter can be exported in CSV format, while the hit sequences can be exported in FASTA format. A graphical display of search results and a summary table display of search results. Entire-contig overviews, showing data layout or coverage information.īlastStation-Free supports megablast, blastn, blastp, and blastx searches allows easy database creation from your FASTA or FASTQ file, which can be compressed in. Search and locate reads by name across entire data sets. Import GFF3 features and quickly find/highlight/display them.

File format support for ACE, AFG, MAQ, SOAP2, SAM and BAM. Tablet - Next Generation Sequence Assembly Visualization - is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. You should check out the help page - Annotating a Genome Using myRAST and Distribution of the SEED server packages The latest Windows or Mac version of the software can be downloaded from here. MyRAST - It is now possible to get a fairly accurate annotation of a prokaryotic genome in about a day using this software package. I have been using this software which permits BLASTN and TBLASTX comparisons on phage sequences in order to define relationships ( Reference: Agren J et al. compare a large number of microbial genomes, give phylogenomic overviews and define genomic signatures unique for specified target groups. Gegenees is a software project for comparative analysis of whole genome sequence data and other Next Generation Sequence (NGS) data. At some point they will be clustered by poreference: The following sites are arranged in the order that I discovered them. Molecular Biology Freeware for Windows Molecular Biology Freeware for WindowsĪ good places to start is Genamics SoftwareSeek.

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