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Sequence Analysis Tools for Molecular Biology

A. Kropinsky Online Analysis Tools
Description: Excellent DNA and protein sequence analysis tools compendium, by Dr. Andrew Kropinski

ABIM Online Analysis Tools
Description: Super comprehensive online sequence analysis tools list

Amos' WWW links page
Description: An exhaustive list of Databases and links to biological resources

exPASy Proteomics tools
Description: One of the major freely accessible Molecular Biology servers. A wide range of tools for sequence analysis

GPSDB
Description: GPSDB (Gene and Protein Synonyms DataBase) is a collection of gene and protein names, organized by species.

NCBI PubMed
Description: The Bio-Medical articles NCBI Database

Swiss Shop
Description: 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.

Pick PCR Primers

Find Oligo in Sequence: Oligo Finder
Description: Allows the localization of an oligonucleotide in a larger sequence

NetPrimer
Description: Comprehensive primer analysis

PCR Links
Description: Provides an excellent selection of Internet resources about the Polymerase Chain Reaction Technique, organized in categories

Primer 3
Description: Pick the best primers from a DNA sequence

Primer X
Description: 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
Description: You can reverse, complement or reverse-complement your sequence. The sequence is cleaned by default from non-GATC characters

DNA-Protein Sequence Randomizer
Description: Basically this is an interface to the Python "random" module. Custom number ofrandomization cycles iterations allowed. Optionally cleans the input sequence with the sequence cleaner before randomization. Optionally formats the output sequence.

EMBOSS nucleotide sequence translation: Transeq
Description: 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.

Open Reading Frame Finder at NCBI
Description: Graphicaly draws the ORFs present in your submitted sequence

Sequence Cleaner
Description: 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 input sequence

Restriction mapping and analysis

Neb Cutter
Description: 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."

Restriction Mapper
Description: "On line restriction mapping the easy way"

WatCut
Description: An on-line tool for restriction analysis, silent mutation analysis, and SNP analysis

Web Cutter
Description: A popular tool for sequence restriction mapping. Also identifies silent restriction sites

BLAST Servers

Batch BLAST at GreenGene
Description: Batch BLAST Database of NCBI

BLAST page at NCBI Entrez
Description: All the BLAST tools you need (except batch BLAST)

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