Tag: SIM

SIM 0.9.4.9 – Peptide Sequence Matching tool

SIM 0.9.4.9

:: DESCRIPTION

SIM (Spectrum Identification Machine) is a Peptide Spectrum Match – PSM search tool that capitalizes on the high intensity b1 fragment ion of tandem mass spectra of peptides coupled in solution with Phenylisotiocyanate – PITC to confidently sequence the first amino acid and ultimately reduce the search space. This tool enables to make a search with sample without PITC labeling too.

::DEVELOPER

Laboratory for Proteomics and Protein Engineering

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • .NET Framework 4.5

:: DOWNLOAD

 SIM

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 15;29(10):1343-4. doi: 10.1093/bioinformatics/btt106. Epub 2013 Feb 27.
Effectively addressing complex proteomic search spaces with peptide spectrum matching.
Borges D1, Perez-Riverol Y, Nogueira FC, Domont GB, Noda J, da Veiga Leprevost F, Besada V, Fran?a FM, Barbosa VC, Sánchez A, Carvalho PC.

SIM – Analyzing long-range RNA-RNA interactions in Viral Genomes and structured RNAs

SIM

:: DESCRIPTION

SilentMutations (SIM) can analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. It simulates destructive and compensatory mutants of two key regions from a single-stranded RNA, which can then be utilized for the combinatorial in vitro analysis of RNA-RNA interactions.

::DEVELOPER

RNA Bioinformatics and High Throughput Analysis Jena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Python
  • numpy
  • viennaRNA

:: DOWNLOAD

SIM

:: MORE INFORMATION

Citation

D. Desiro, M. Hölzer, B. Ibrahim, and M. Marz,
SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs
Virus Res. 2019 Jan 15;260:135-141. doi: 10.1016/j.virusres.2018.11.005. Epub 2018 Nov 12.

SIM – Cell- and Gene-based Computer Model for Mammalian Somitogenesis

SIM

:: DESCRIPTION

SIM is a software of cell- and gene-based computer model for mammalian somitogenesis, simulating a gene regulatory network combining clock (Hes1/7) and gradient (Tbx6, Fgf8, Wnt3a) with Delta/Notch signaling resulting in dynamic gene expression patterns as observed in vivo finally leading to boundary formation.

::DEVELOPER

Institute of Experimental Genetics , German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

SIM

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java 

:: DOWNLOAD

 SIM

:: MORE INFORMATION

Citation

Tiedemann HB, Schneltzer E, Zeiser S, Hoesel B, Beckers J, Przemeck GKH, Hrabě de Angelis M. (2012).
From dynamic Expression patterns to Boundary Formation in the Presomitic mesoderm
PLoS Comput Biol 8(6): e1002586. doi:10.1371/journal.pcbi.1002586