Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. This web server makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist. Extensive user documentation applicable to any public or local Galaxy instance is available. Offers a huge varierty of tools for analysis and file interconversion.
Sequence conversion (Bioinf @ Bugaco) - a huge suite of conversion tools. Also try Conversion
Readseq developed by D.G. Gilbert (Indiana University) reads and converts biosequences between a selection of common biological sequence formats, including EMBL, GenBank and fasta sequence formats is available here .
EMBOSS Seqret reads and writes (returns) sequences. It is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.
Sequence editor - Convert DNA and RNA sequences. Generate antiparallel, complement and inverse sequences.
Format Converter v2.2.5 - This program takes as input a sequence or sequences (e.g., an alignment) in an unspecified format and converts the sequence(s) to a different user-specified format. Also converts *.gbk to *.gff3.
ApolloRNA Convert data - Transformation of TransTermHP, CRISPRfinder, MOSAIC, PatScan, DARN! (GFF), GenBank output data in GFF and GAME XML format data that can be read by Apollo.
GenBank 2 Sequin (P. Lehwark & S. Greiner, Max-Planck Institute for Molecular Plant Physiology, Germany) - this extremely usesful program is designed to convert revised GeSeq output into the Sequin format, required for NCBI submission. None the less, any custom GenBank file can be prepared for NCBI submission using GenBank 2 Sequin.
JaMBW (European Molecular Biology Laboratory of Heidelberg, Germany). Java based Molecular Biologist's Workbench.Select Chapter 1 for sequence format conversion (upper lower case; T U; reverse or complement sequence).
Nucleic Acid Sequence Massager (Allotron Biosensor Corporation) which in addition to removing spurious material (numbers, breaks, HTML, spaces) changes the format (upper to low case, complement, reverse, RNA to DNA, and triplets).
Segmenter (C. Laing, Public Health Agency of Canada) - this bit of code is extremely useful it you want to fragment a phage genome into 10-20 kb pieces for BLASTX analysis if looking for framshifts.
extractUpStreamDNA (A. Villegas, Public Health Ontario) - takes a Genbank flatfile (*.gbk) as input and parses through and for every CDS that it finds, it extracts a pre-determined length of DNA upstream (length will be an argument; and will include 3 nt for the initiation codon). Output will be an FFN file of these upstream DNA sequences. N.B. this only WORKS for prokaryotic sequences because it does not handle Splits or Joins found in eukaryotic. This data then can be analyzed with programs such as MEME.This program is temporarily unavailable online, though one can download it from here.
Convert GenBank to Fasta (G. Rocap, School of Oceanography, University of Washington, U.S.A.) - Select a GenBank formatted file containing a feature table. Select whether to extract translated peptide sequences, DNA sequence for each feature, or the entire DNA sequenceof the whole record. If you chose "Peptide Sequence", your feature table must have "translation"sub-features.
FaBox (Palle Villesen Fredsted, Aarhus University, Denmark) - an online fasta sequence toolbox, including Fasta header editor, Fasta header replacer, Fasta sequence extractor, Fasta sequence subtractor, Fasta sequence joiner, Fasta dataset splitter/divider
FeatureExtract - this very useful service extracts sequence and feature annotation, such as intron/exon structure, from GenBank entries and other GenBank format files. (Reference: R. Wernersson. 2005. Nucl. Acids Res. 33 ( Web Server issue): W567-W569). Also possible is extraction of 5' and 3' sequences.
Sequence editor - carries out numerous functions:
Antiparallel - Create the antiparallel DNA or RNA strand. For example the sequence ATGC will be converted into GCAT. It is a combination of the both functions Complement and Inverse.
Complement - Create the complement DNA or RNA strand. For example the sequence ATGC will be converted into TACG.
Inverse - Create the inverse DNA or RNA strand. For example the sequence ATGC will be converted into CGTA.
T to U - Replace all thymidine by uracil. For example the sequence ATUGC will be converted into AUUGC.
U to T - Replace all uracil by thymidine. For example the sequence ATUGC will be converted into ATTGC.
UCase - Convert the sequence into upper case.
LCase - Convert the sequence into lower case.
Shuffle DNA and Sequence Randomizer permit one to randomize a sequence to compare with one's own.