:: DESCRIPTION
MotifIndexer is a comprehensive strategy for de novo identification of DNA regulatory motifs at a genome level.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M and Dinesh-Kumar SP. (2012)
Discovery of stress responsive DNA regulatory motifs in Arabidopsis.
PLoS ONE 7:e43198
:: DESCRIPTION
Multi-Dendrix is an algorithm for the simultaneous discovery of multiple driver pathways using only somatic mutation data from a cohort of samples. Multi-Dendrix uses an integer linear program to identify pathway sets such that each pathway contains genes with approximately mutually exclusive mutations and high coverage of the sample set.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
M.D.M. Leiserson, D. Blokh, R. Sharan, B.J. Raphael. (2013)
Simultaneous Identification of Multiple Driver Pathways in Cancer.
PLoS Comp Bio, 9(5):e1003054
:: DESCRIPTION
MetaSPS was shown to yield the longest and most accurate de novo sequences from tandem mass spectrometry data at nearly full sequence coverage.
::DEVELOPER
Nuno Bandeira , Adrian Guthals [aguthals (at) cs.ucsd.edu] ,CCMS The Center for Computational Mass Spectrometry
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Cell Proteomics. 2012 Oct;11(10):1084-96. Epub 2012 Jul 13.
Shotgun protein sequencing with meta-contig assembly.
Guthals A1, Clauser KR, Bandeira N.
:: DESCRIPTION
UniNovo is a universal de novo peptide sequencing tool that works well for various types of spectra and spectral pairs (e.g., CID, ETD, HCD, CID/ETD, etc). The accuracy of de novo reconstructions generated by UniNovo is better than or comparable to PepNovo+ or PEAKS. Moreover, UniNovo also estimates the error rate of the reported reconstruction.
::DEVELOPER
CCMS The Center for Computational Mass Spectrometry
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Aug 15;29(16):1953-62. doi: 10.1093/bioinformatics/btt338. Epub 2013 Jun 12.
UniNovo: a universal tool for de novo peptide sequencing.
Jeong K1, Kim S, Pevzner PA.
:: DESCRIPTION
Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.
::DEVELOPER
INRA, URGI
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tedna: a Transposable Element De Novo Assembler.
Zytnicki M, Akhunov E, Quesneville H.
Bioinformatics. 2014 Jun 3. pii: btu365.
:: DESCRIPTION
NPLB is an efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide TSSs, without relying on known promoter elements.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites.
Mitra S, Narlikar L.
Bioinformatics. 2015 Nov 2. pii: btv645.
:: DESCRIPTION
Famdenovo is an algorithm that calculates the probability of de novo status in deleterious germline mutations using family history data.
::DEVELOPER
Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gao F, Pan X, Dodd-Eaton EB, Recio CV, Montierth MD, Bojadzieva J, Mai PL, Zelley K, Johnson VE, Braun D, Nichols KE, Garber JE, Savage SA, Strong LC, Wang W.
A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome.
Genome Res. 2020 Aug;30(8):1170-1180. doi: 10.1101/gr.249599.119. Epub 2020 Aug 18. PMID: 32817165; PMCID: PMC7462073.
:: DESCRIPTION
Anchor is a set of tools for making automated improvements to de novo assemblies.
Anchor currently includes two main modules:
– Correction of erroneous single-nucleotide variants and small indels
– Scaffold-filling by local re-assembly
::DEVELOPER
Canada’s Michael Smith Genome Sciences Centre
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
TBNovo is a de novo protein sequencing software tool which combines both top down and bottom up tandem mass spectra.
::DEVELOPER
Xiaowen Liu ,CCMS The Center for Computational Mass Spectrometry
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Proteome Res. 2014 Jul 3;13(7):3241-8. doi: 10.1021/pr401300m. Epub 2014 Jun 18.
De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.
Liu X1, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolić N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, Paša-Tolić L, Pevzner PA.
