Source: seqtools Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: science Priority: optional Build-Depends: debhelper-compat (= 13), libgtk2.0-dev, libsqlite3-dev, libcurl4-openssl-dev | libcurl4-dev, libjsoncpp-dev, d-shlibs Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/seqtools Vcs-Git: https://salsa.debian.org/med-team/seqtools.git Homepage: https://www.sanger.ac.uk/science/tools/seqtools Rules-Requires-Root: no Package: libgbtools0 Architecture: any Multi-Arch: same Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Description: library for visualising sequence alignments The SeqTools package contains three tools for visualising sequence alignments: Blixem, Dotter and Belvu. . This package contains the library all three tools are linked against. Package: libgbtools-dev Architecture: any Multi-Arch: same Section: libdevel Depends: libgbtools0 (= ${binary:Version}), ${devlibs:Depends}, ${misc:Depends} Description: library for visualising sequence alignments (devel) The SeqTools package contains three tools for visualising sequence alignments: Blixem, Dotter and Belvu. . This package contains the static library and header files. Package: belvu Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Breaks: acedb-other-belvu (<< 4.9.39+dfsg.02-2) Provides: acedb-other-belvu Replaces: acedb-other-belvu (<< 4.9.39+dfsg.02-2) Description: multiple sequence alignment viewer and phylogenetic tool Belvu is a multiple sequence alignment viewer and phylogenetic tool with an extensive set of user-configurable modes to color residues. . * View multiple sequence alignments. * Residues can be coloured by conservation, with user-configurable cutoffs and colours. * Residues can be coloured by residue type (user-configurable). * Colour schemes can be imported or exported. * Swissprot (or PIR) entries can be fetched by double clicking. * The position in the alignment can be easily tracked. * Manual deletion of rows and columns. * Automatic editing of rows and columns based on customisable criteria: - removal of all-gap columns; - removal of all gaps; - removal of redundant sequences; - removal of a column by a user-specified percentage of gaps; - filtering of sequences by percent identity; - removal of sequences by a user-specified percentage of gaps; - removal of partial sequences (those starting or ending with gaps); and - removal of columns by conservation (with user-specified upper/lower cutoffs). * The alignment can be saved in Stockholm, Selex, MSF or FASTA format. * Distance matrices between sequences can be generated using a variety of distance metrics. * Distance matrices can be imported or exported. * Phylogenetic trees can be constructed based on various distance-based tree reconstruction algorithms. * Trees can be saved in New Hampshire format. * Belvu can perform bootstrap phylogenetic reconstruction. Package: blixem Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: interactive browser of sequence alignments Blixem is an interactive browser of sequence alignments that have been stacked up in a "master-slave" multiple alignment; it is not a 'true' multiple alignment but a 'one-to-many' alignment. . * Overview section showing the positions of genes and alignments around the alignment window * Detail section showing the actual alignment of protein or nucleotide sequences to the genomic DNA sequence. * View alignments against both strands of the reference sequence. * View sequences in nucleotide or protein mode; in protein mode, Blixem will display the three-frame translation of the reference sequence. * Residues are highlighted in different colours depending on whether they are an exact match, conserved substitution or mismatch. * Gapped alignments are supported, with insertions and deletions being highlighted in the match sequence. * Matches can be sorted and filtered. * SNPs and other variations can be highlighted in the reference sequence. * Poly(A) tails can be displayed and poly(A) signals highlighted in the reference sequence. Package: dotter Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Breaks: acedb-other-dotter (<< 4.9.39+dfsg.02-2) Provides: acedb-other-dotter Replaces: acedb-other-dotter (<< 4.9.39+dfsg.02-2) Description: detailed comparison of two genomic sequences Dotter is a graphical dot-matrix program for detailed comparison of two sequences. . * Every residue in one sequence is compared to every residue in the other, and a matrix of scores is calculated. * One sequence is plotted on the x-axis and the other on the y-axis. * Noise is filtered out so that alignments appear as diagonal lines. * Pairwise scores are averaged over a sliding window to make the score matrix more intelligible. * The averaged score matrix forms a three-dimensional landscape, with the two sequences in two dimensions and the height of the peaks in the third. This landscape is projected onto two dimensions using a grey-scale image - the darker grey of a peak, the higher the score is. * The contrast and threshold of the grey-scale image can be adjusted interactively, without having to recalculate the score matrix. * An Alignment Tool is provided to examine the sequence alignment that the grey-scale image represents. * Known high-scoring pairs can be loaded from a GFF file and overlaid onto the plot. * Gene models can be loaded from GFF and displayed alongside the relevant axis. * Compare a sequence against itself to find internal repeats. * Find overlaps between multiple sequences by making a dot-plot of all sequences versus themselves. * Run Dotter in batch mode to create large, time-consuming dot-plots as a background process.