Biochemistry databases & software
Databases
Transterm. The translation control database.
Imprinted Gene Catalogue A catalogue of imprinted genes and parent-of-origin effects in humans and animals.
Retrobase. Database of transposable genetic elements.
Software - developed by Dr Peter Stockwell
SSEdit(~11Mb dmg file) - Single (Short) Sequence Editor
A MacOS X application for viewing and editing single sequences. Input
and output files in FASTA, NRBF, Staden and other formats are
supported with the capability to recognise some by the file extension
name. SSedit will display nucleic acid sequences in double stranded
form, can reverse and complement the sequence and can translate to
peptide sequences using various genetic codes including user-created
ones. Sequences of arbitrarily large length can be processed, limited
by available memory on the computer. Search functions are provided
and printer listings and screen displays can be controlled
extensively. External sequences can be inserted in whole or in part
into the main sequence at the active position. SSedit v6.08 works
with MacOS 10.5 (Leopard) or later and is distributed as a universal
application. Documentation is included.
Homed(~11Mb dmg file) - HOMologous sequence EDitor
A MacOs X application for displaying and editing multiple sequence
alignments. A considerable number of MSA formats are supported,
including Nexus, Phylip and Clustal. Nucleic acid alignments can be
displayed and edited as the corresponding peptide translation, using
all usual and user-specified genetic codes. Furthermore, in order to
maintain nucleic acid alignments on codon boundaries, it is possible
to take a set of nucleic acids, export them as a peptide set which can
be aligned by usual multiple alignment applications, then imprint the
gapping back on to the original nucleic acid set. This process is
often needed in phylogenetic work where a nucleic acid multiple
alignment will not preserve the codon boundaries of the encoded
peptide.
Homed allows various uses of colour, for showing a range of parameters
for different amino acid residues or for highlighting specific
residues: various colour control functions are provided for this.
Alternatively, portions of individual sequences or of the complete
alignment can be coloured as blocks to indicate structural or
functional domains. using information that is contained in textual
files that can be saved from the application or optionally created or
modified manually.
Homed is not a multiple sequence aligner, but will allow a new
sequence to be manually edited to conform to an existing alignment.
Substantial control is available for the appearance of printer
listings and screen displays with the ability to reorder sequences and
other elements of the display by dragging and dropping. Interfacing
with the MacOS printing system allows Homed to write listings as pdf
files, complete with any colour features that have been set.
Homed has no formal limits for the number of sequences or their
lengths, although very large sets will take appreciable time to load
and modify on edits. However, available memory on the computer will
cause some upper limit. Homed v6.8 works with MacOS 10.5 (Leopard) or
later and is distributed as a universal application. Documentaton is
included.