Useful Online software

DNA Online Tools

Description

AMIGene  Annotation of Microbial Genes
Benchling  Online tools for vector editing, restriction analysis, primer search, multi-sequence alignment, and more.
Clustal Omega Multiple sequence alignment of DNA or protein sequences. Clustal Omega replaces the older ClustalW alignment tools.
Countcodon Generates a codon usage table for the input sequence.
CpGplot Program to plot CpG rich areas in a nucleic acid sequence
DNAWorks A web tool for optimizing melting temperature during gene synthesis.
EGassember Aligns and merges sequence fragments resulting from shotgun sequencing or gene transcripts (EST) fragments in order to reconstruct the original segment or gene
ENA The European Nucleotide Archive (ENA) provides a comprehensive record of the world’s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation
GeneMark A family of gene prediction programs, Eucaryotes; Bacteria; viruses…
Genome Compiler Allows you to manipulate genetic information; from genes to plasmids to whole genomes. You can rapidly access extensive libraries of genetic parts, and easily order your final design from a variety of providers.
GeneDesign Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
Genscan Predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.
make-na Automatic production of DNA double helix with sequence input.
NEB Cutter Tool for finding restriction sites.
ORF Finder ORF Finder (Open Reading Frame Finder).
RNA/DNA secondary structure prediction and design PairFold predicts the minimum free energy secondary structure formed by two input DNA or RNA molecules.

PROTEINS Online Tools

Description

BLAST Fast local similarity search tool for protein sequence databases.
Clustal Omega Multiple sequence alignment of DNA or protein sequences. Clustal Omega replaces the older ClustalW alignment tools.
DeepView Program for viewing and studying protein structure.
ExPASy SIB Bioinformatics Resource Portal.
Modeller For homology or comparative modeling of protein three-dimensional structures.
Protein Data Bank in Europe The European resource for the collection, organisation and dissemination of 3D structural data (from PDB and EMDB) on biological macromolecules and their complexes.
UniProt Comprehensive resource for protein sequence and functional annotation data.
Zinc Finger Tools Design a Zinc Finger Protein.