:: DESCRIPTION
Sequence Analysis is a collage of coding projects which the author has written over the past several years for various clients in his work as a bioinformatics consultant
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:: DESCRIPTION
Serial Cloner has been developed to provide a light molecular biology software to both Macintosh and Windows users. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format. Serial Cloner also import files saved in the Vector NTI, ApE, pDRAW32 and GenBank formats. Import from MacVector is also possible now. Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. Serial Cloner handles Annotations and Features both in the sequence and in the Graphic Map.
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Mosaic is a software application to visually analyze sequence relationships. The similarities between the sequences of a given set are displayed within a matrix (mosaic plot), which enables the visual identification of clusters of related sequences, outliers or other sequences with special properties.
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N/A
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Citation
Stefan R. Maetschke, Karin S. Kassahn, Jasmyn A. Dunn, Siew P. Han, Eva Z. Curley, Katryn J. Stacey, Mark A. Ragan
A visual framework for sequence analysis using n-grams and spectral rearrangement
Bioinformatics. 2010 Mar 15;26(6):737-44. doi: 10.1093/bioinformatics/btq042
:: DESCRIPTION
PSAAM (Protein Sequence Analysis And Modelling) includes many useful features for analysis of structural information from sequence data, cartoons for graphical representation of secondary structures, prediction programs, and prediction aids, a ribosome function for generation of coordinates sets in PDB format (including Header information) for viewing by molecular graphics packages (examples, see also PDVWIN), and a SeqPlot function for plotting secondary structural models (helical cylinders and wheels, coils, etc., with each residue indicated by a circle, color-coded (or coded by line thickness) according to the current physico-chemical index.
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Mussa (Multi-Species Sequence Analysis) is a bioinformatics tool for finding and visualizing regions of conserved DNA by comparing across several species. It has been found that conserved regions are frequently enriched for regions that are functionally important. Thus Mussa is a tool to help discover previously unknown functional DNA elements.
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Pse-Analysis is a Python package for DNA/RNA and protein/peptide sequence analysis based on pseudo components and kernel methods.
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N/A
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Citation
Liu B, Wu H, Zhang D, Wang X, Chou KC.
Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods.
Oncotarget. 2017 Feb 21;8(8):13338-13343. doi: 10.18632/oncotarget.14524. PMID: 28076851; PMCID: PMC5355101.
:: DESCRIPTION
AAscan, PCRdesign and MutantChecker is a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.
AAScan (formely AlaScan) – batch primer design software for scanning mutagenesis
MutantChecker – helps to analyse the sequenceing results from scanning mutagenesis
PCR Cloning – design of primers for ligation-independent cloning
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Laboratory of Biomolecular Research (LBR)
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Citation
PLoS One. 2013 Oct 30;8(10):e78878. doi: 10.1371/journal.pone.0078878. eCollection 2013.
AAscan, PCRdesign and MutantChecker: a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.
Sun D1, Ostermaier MK, Heydenreich FM, Mayer D, Jaussi R, Standfuss J, Veprintsev DB.
:: DESCRIPTION
BW4SA is a generic, practical, versatile library for implementing a variety of (bio)sequence analysis algorithms in succinct space.
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GSA (Genome-scale algorithmics) group
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N/A
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Citation
Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
Versatile succinct representations of the bidirectional Burrows-Wheeler transform.
ESA 2013, Springer, Lecture Notes in Computer Science Volume 8125, 2013, pp 133-144
:: DESCRIPTION
CAFE is a standalone software for efficient calculation of 28 alignment-free dissimilarity measures.
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Citation
Lu YY, Tang K, Ren J, Fuhrman JA, Waterman MS, Sun F.
CAFE: aCcelerated Alignment-FrEe sequence analysis.
Nucleic Acids Res. 2017 Jul 3;45(W1):W554-W559. doi: 10.1093/nar/gkx351. PMID: 28472388; PMCID: PMC5793812.
:: DESCRIPTION
CloVR is a desktop application that integrates state-of-the-art genomic tools in a robust, user friendly, and fully automated software package with optional support for cloud computing platforms. CloVR currently bundles push-button pipelines for microbial genomics, including single-genome projects, 16S rRNA sequence analysis, and metagenomic sequencing projects. Additional pipelines for comparative genome analysis, prokaryotic and eukaryotic RNA-sequencing and viral genomics are planned.
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Institute for Genome Sciences , University of Maryland School of Medicine
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Citation:
Angiuoli SV, Matalka M, Gussman G, Galens K, Vangala M, Riley DR, Arze C, White JR, White O and Fricke WF.
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing.
BMC Bioinformatics. 2011 Aug;12:356.
