QPARSE – searching for degenerate, long-looped or multimeric G-quadruplexes
QPARSE is a Python program (Python v. 2.7) that allows to search for exact or degenerate putative patterns associated with the formation of four-stranded non-canonical nucleic-acids structures (quadruplex or PQS) and multimeric quadruplex structures. The tool can also assess the symmetrical properties of the linking loops to evaluate the potential of longer loops (>= 6 nt) to form hairpins that stabilize the quadruplex structure.
- The tool can detect both exact or degenerate islands (i.e. islands containing any desired combination of bases and bulges, and mismatched islands).
- The tool can detect longer PQS with more than four consecutive islands that can potentially form multimeric quadruplexes.
- The tool is exhaustive in the search and all the possible combinations of the detected islands are considered.
- The tool can assess the symmetrical properties (mirror, palindromic or a combination of both) of the linking loops to evaluate the potential formation of hairpin structures that stabilize longer loops (>= 6 nt).
- The search is not limited to G or C but can be extended to any other base.
Go to the web-server or get the tool source code on github.
FunταξΙΣ
FunταξΙΣ web server is the first attempt to automatically infer which functional specificities and commonalities exist among different taxa. The algorithm considers Gene Ontology terms and their frequencies found in GOA database. Since annotations are linked to proteins, the frequencies of GO terms can be associated to the species which the proteins belong to. This association between GO terms and taxa is exploited to infer which terms are allowed or forbidden for annotating proteins of a particular taxon, providing a set of constraints between them. Due to lack of annotation for the majority of species, the taxonomic tree is reduced by collapsing all branches to a generic level of taxonomy (class level) and the algorithm exploits this higher hierarchical membership of taxonomy. Since the constraints nearly cover the whole taxonomy, it is also possible to obtain the mapping of a function over the taxonomy and, consequently, the tool can be used:
- to discover how functional knowledge is distributed over taxa
- to discover if there is an unexpected missing functional knowledge for some taxa
- to detect improper/erroneous associations between taxa and functions
Publication: M. Falda, E. Lavezzo, P. Fontana, L. Bianco, M. Berselli, E. Formentin, S. Toppo: ”Eliciting the Functional Taxonomy from protein annotations and taxa”. Scientific reports, 6, 31971; 2016.
Argot 2.5
Argot2.5 (Annotation Retrieval of Genel Ontology Terms) is an enhancement of previous server Argot2 able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate. These hits may be obtained by different methods as BLAST, HMMER and so on. In the present web server we allow users to interact with Argot2.5 in different ways according to specific needs and expertise.
The new features implemented in the web server are:
- word and bigrams clouds of functional predicted Gene Ontology terms to ease the readability of the results
- a clustered version of Uniprot for Blast searches in order to remove redundancy and speed up searching time
- a novel semantic similarity measure, called simGIC
- an extended set of taxonomic constraints applied according to the automatic in-house developed tool FunταξΙΣ, that expands the list provided by Gene Ontology Consortium (GOC)
Publication: E. Lavezzo, M. Falda, P. Fontana, L. Bianco, S. Toppo: ”Enhancing protein function prediction with taxonomic constraints–The Argot2.5 web server”. Methods, 93, 15-23; 2016.
Argot 2
Argot2 (Annotation Retrieval of Genel Ontology Terms) is a tool that is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate. These hits may be obtained by different methods as BLAST, HMMER and so on. In the present web server we allow users to interact with Argot2 in different ways according to specific needs and expertise.
Publication: M. Falda, S. Toppo, A. Pescarolo, E. Lavezzo, B. Di Camillo, A. Facchinetti, E. Cilia, R. Velasco, P. Fontana: ”Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms”. BMC Bioinformatics, 13, S14; 2012.
keeSeek
keeSeek is a command line tool that uses Graphics cards for generating, for a given reference genome, a set of k-mers absent in that genome. We call them neverwords.
Publication: M. Falda, P. Fontana, L. Barzon, S. Toppo, E. Lavezzo: ”keeSeek: searching distant non-existing words in genomes for PCR-based applications”. Bioinformatics, 30, 2662-2664; 2014.
Pathway Inspector
Pathway Inspector is a web application developed in collaboration with the Edmund Mach Foundation, Trento, Italy. It is designed for helping researchers to find patterns of expression in complex RNA-seq experiments. The tool combines two standard approaches for RNA-seq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad-hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology.
Publication: L. Bianco, S. Riccadonna, E. Lavezzo, M. Falda, E. Formentin, D. Cavalieri, S. Toppo, P. Fontana: ”Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms”. Bioinformatics; 2016.
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MPA – Multiple Peak Alignment
MPA is a software able to generate a multiple alignment of chromatographic peaks from proteomic profiles. There is not a currently simple way to make easy comparisons of data from multiple proteome profiles and yet most experiments contain more than two samples. MPA has been developed to answer these needs and ease the work of users in multiple comparisons among profiles data. MPA has been specifically developed on the basis of the output data produced by the ProteomLab PF2D platform but, in principle, is able to align peaks of chromatographic profiles coming from other sources.
Publication: S. Toppo, A. Roveri, M. P. Vitale, M. Zaccarin, E. Serain, E. Apostolidis, M. Gion, M. Maiorino, F. Ursini: ”MPA: A multiple peak alignment algorithm to perform multiple comparisons of liquid-phase proteomic profiles”. Proteomics, 8, 250-253; 2008
NeSSie – nucleic-acids elements of sequence symmetry identification
NeSSie is a c/c++ 64 bit program that allows to perform fast patterns search and sequence analyses on DNA strings using the NeSSie library. The tool currently allows to perform several types of DNA sequence analyses at once such as:
- de novo search for motifs with a mirror or palindromic symmetry, as well as motifs with a DNA-triplex forming potential (both perfect and degenerated motifs)
- exhaustive search for all k-mers in the sequence
- calculation of the sequence complexity and entropy on the full sequence, or using a sliding window of given size and shift
- search for exact motifs from a provided list
The tool can be used out of the box, however, the library is far richer and the source code is provided. This makes the library easy to expand or bundle with other programs, providing a source of utilities to people interested in performing analyses of genomes at the sequence level.
Publication: Michele Berselli, Enrico Lavezzo, Stefano Toppo; NeSSie: a tool for the identification of approximate DNA sequence symmetries, Bioinformatics, bty142, https://doi.org/10.1093/bioinformatics/bty142