rNA (randomized Numerical Aligner) is a software able to align the huge amount of data produced by Next Generation Sequencers. The main feature of rNA is the fact that it achieves an accuracy greater than the majority of other tools in a feasible amount of time. rNA works with single as well as paired ends reads and it allows indels and delta-search for better accuracy. A graphical user interface is provided for not command-line-skilled users and an MPI-based version for cluster is in development.
rNA executables and source code are freely downloadable on SourceForge.
COREFINDER is a software that allows sorting out a core collection from a large database of individual molecular profiles. Read the tutorial or download the software
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
The IGA's BLAST service allows to find local similarity with the Vitis Vinifera DNA sequences database.
Repeated Sequences annotation for Vitis Vinifera public gbrowse server.
The ABIF file format is a binary format for storing data, developed by Applied Biosystems, Inc.
The Bio::Trace::ABIF Perl module provides general methods for accessing any chunk of information contained into an ABIF file. Besides, it provides shortcut methods for reading the most commonly used parts of the file, and methods for manipulating the data (e.g., for computing LOR scores).
SMaRTFinder is a command line tool to search biosequences for structured motifs (or structured models), that is lists of patterns separated by distance intervals. It reads a sequence in FASTA format and a structured model specification, either from a file or from the standard input, then searches for exact/approximate occurrences of the structured model (in one or both strands, if the sequence is DNA) and outputs a file in GFF format, which can be visualized, for instance, by Apollo.
LadderFinder is a program designed to solve a problem in DNA genotyping. It helps in the construction of allelic ladders that drive the sizing and binning of SSR fragments produced by PCR. The algorithm scans a spreadsheet containing a database of individual profiles and finds a minimum set of individuals, that covers the maximum number of alleles represented in the database, with all alleles represented only once. The last constraint is imposed to make homogeneous the ladder peaks in the pherograms. Given such a constrain, the best solution may not include all alleles.
Matchfinder computes a maximal matching of a graph. A matching of a graph G is a set of pairwise non-adjacent edges of G. A maximal matching for G is a matching of maximum cardinality with respect to G. Notice that there can be many different maximal matchings for a single graph. For instance, the graph G=( V={1, 2, 3}, E={(1,2), (2,3)} has two maximal matchings: M={(1,2)} and M={(2,3)}.
FingerPrint Background removal
We implemented a new data-independent tool, FPB (FingerPrint Background removal), suitable for large scale projects as well as mapping of few clones.
GAM is a free parallel software tool to integrate two different assemblies and improves the overall quality of the genome sequences by merging them. It discovers and align similar sequences by using the positions of placed reads. An order sequence of reads contiguous on the same contig is called frame. When the same frame is shared by both original assemblies, GAM dubs it block.
GAM deduces block orders from assembly read orders and, by using them, builds a graph of assemblies whose nodes represent blocks and whose edges represents block order. Since cycles in the graph of assemblies denote conflicting block order in assemblies, GAM avoid to merge sequences containing blocks belonging to them.
