Staden Package is a fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
On the Gap4 front there have been several minor joining related
improvements in how it scores joins in Find Internal Joins and the
functionality of the align button in the Join Editor.
Also of consequence to gap4 are the various changes to io_lib (the
library for all I/O to various trace file formats). With the addition
of a new hash_exp program it now allows for experiment files to be
concatenated together and indexed. The list of experiment file names
should stil be supplied to gap4, but provided the EXP_PATH environment
variable has been set correctly gap4 will be able to fetch individual
sequences out of the concatenated experiment file
archive. Improvements to the user interface for this still need to be
454 SFF archives are now better supported. The defsult 454 indices
now work, although the hash_sff program can be used to provide an
alternative indexing strategy (possibly faster in some cases).
Gap4 and trev also have another trace display style for traces that
have 1 sample scan (x4 channels) per base call. In this case it can
also draw 4 confidence values instead of 1 per base. These abilities
will allow better integration of Solexa traces when more readily
Plus of course the usual mix of bug fixes and minor tweaks. See the
full change log for details (via the SourceForge site).
Other notable changes
· Various SNP Candidates improvements. The "correlation offset" is now
adjustable (this controls the average correlation score needed
before groups are considered for automatic merging). SNP base calls
now work by generating a consensus rather than requiring 100%
identity. it now skips sequences containing a REFS note. Merging can
be forced until the number of groups is less than or equal to a
predetermined amount (NB: not usually ideal).
· Shuffle pads now has a "band size" parameter for the alignments.
Also bug fixed in various places.
· The old editor shuffle command has been replaced by strip pads. It
now only removes entire columns of pads and does no pad movement at
· The join editor align button will now cope better with handling long
alignments in repeated data, hopefully avoiding the "too long for
practical use of dynamic programming" message in such cases.
It also now has "" buttons either side of the "Align"
button. These anchor one end of the alignment to the current overlap
position and then only align from that point leftwards or
rightwards. This helps to force an alignment to anchor at a specific
location which is useful when aligning data consisting of multiple
· Alignments found by Find Internal Joins now take into account the
alignment score in addition to the percentage identity. This means
that no longer will a 100bp overlap at 100% identity be considered
as a better overlap than a 2kb overlap at 99% identity.
· The Contig Navigation window now has Page Up and Page Down
keybindings for previous and next match. It also has the ability to
automatically display traces at the appropriate regions using the
contig editors "Auto-display traces" functionality.
· The "View List" window now has a Save button.
· New programs: hash_exp, hash_sff, append_sff, extract_fastq.
· Added TRACE_PATH and EXP_PATH environment variables to use in
preference to RAWDATA (when defined).
· Now uses libcurl instead of wget for much faster web based trace