The Bio-Web: Molecular and Cell Biology and Bioinformatics news, tools, books, resources and web applications development
Sequence Analysis Tools and Databases for Molecular Biology and Bioinformatics
EBI Sequence Analysis Tools
A comprehensive suite of online Bioinformatics tools, including tools for the analysis and comparison of nucleotide and protein sequences, data from functional genomics experiments, text mining of the scientific literature and tools for determination and visualisation of macromolecular structures.
All these tools can be accessed over the web and most provide Web Services interfaces using SOAP or REST APIs.
Amos' WWW links page
An exhaustive list of Databases and links to biological resources
exPASy Proteomics tools
One of the major freely accessible Molecular Biology servers. A wide range of tools for sequence analysis
NCBI PubMed
The Bio-Medical articles NCBI Database
Swiss Shop
Swiss-Shop is a service that allows you to automatically obtain (by email), on a regular schedule, new sequence entries relevant to your field(s) of interest
UGENE
UGENE is a free cross-platform genome analysis suite. It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install
SequencEasy
A basic yet original DNA sequence analysis and manipulation tool
EMBOSS Explorer
A graphical online user interface to the EMBOSS suite of bioinformatics tools
The Galaxy Project
Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
PCR Links
Provides an excellent selection of Internet resources about the Polymerase Chain Reaction Technique, organized in categories
Primer 3
Pick the best primers from a DNA sequence
Primer X
PrimerX is a web-based program written to automate the design of mutagenic PCR primers for site-directed mutagenesis. Based on your input, PrimerX compares a template DNA sequence with a DNA or protein sequence that already incorporates the desired mutation. It then generates forward primer sequences by computing for all possible oligonucleotide sequences of appropriate length that encode this mutation and follow your specified constraints. Finally, PrimerX generates corresponding reverse primer sequences, and computes for other necessary information such as melting temperature and GC content for each primer pair.
Basic sequence manipulation tools
DNA sequence reverse-complement tool
You can reverse, complement or reverse-complement your sequence. The sequence is cleaned by default from non-GATC characters
DNA-Protein Sequence Randomizer
Basically this is an interface to the Python "random" module. Custom number of randomization cycles iterations allowed. Optionally cleans the input sequence with the sequence cleaner before randomization. Optionally formats the output
sequence.
EMBOSS nucleotide sequence translation: 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
Sequence Cleaner
Allows the easy cleaning (removal of unwanted spaces, slashes, numbers etc..) of sequences. Tipically useful when retrieving sequences from online databases. Also allows custom numbering of the output sequence
Neb Cutter
Excellent tools. NEB says:"This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and "submit". Further options will appear with the output."
