Staden Package Staden Package is a fully developed set of DNA sequence assembly, editing and analysis tools.
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data analyzer sequence assembly DNA DNA sequence sequence assembly

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Staden Package is a fully developed set of DNA sequence assembly, editing and analysis tools. 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 relatedimprovements in how it scores joins in Find Internal Joins and thefunctionality of the align button in the Join Editor.Also of consequence to gap4 are the various changes to io_lib (thelibrary for all I/O to various trace file formats). With the additionof a new hash_exp program it now allows for experiment files to beconcatenated together and indexed. The list of experiment file namesshould stil be supplied to gap4, but provided the EXP_PATH environmentvariable has been set correctly gap4 will be able to fetch individualsequences out of the concatenated experiment filearchive. Improvements to the user interface for this still need to bemade.454 SFF archives are now better supported. The defsult 454 indicesnow work, although the hash_sff program can be used to provide analternative indexing strategy (possibly faster in some cases).Gap4 and trev also have another trace display style for traces thathave 1 sample scan (x4 channels) per base call. In this case it canalso draw 4 confidence values instead of 1 per base. These abilitieswill allow better integration of Solexa traces when more readilyavailable.Plus of course the usual mix of bug fixes and minor tweaks. See thefull change log for details (via the SourceForge site).Other notable changesGap4· 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 Also bug fixed in various places.· The old editor shuffle command has been replaced by strip pads.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 all.· 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 repeat elements.· 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.Io_lib· 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 fetching.

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