tRNAmodpred – Predicting Posttranscriptional Modifications in tRNAs

tRNAmodpred

:: DESCRIPTION

tRNAmodpred is a method for predicting modifications in tRNA using the MODOMICS database of RNA modification pathways as a reference.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 tRNAmodpred

:: MORE INFORMATION

Citation:

tRNAmodpred: a computational method for predicting posttranscriptional modifications in tRNAs.
Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM.
Methods. 2016 Mar 22. pii: S1046-2023(16)30047-0. doi: 10.1016/j.ymeth.2016.03.013.

GENEHUNTER++sad – Modification of Genehunter to allow for the Sad score

GENEHUNTER++sad

:: DESCRIPTION

GENEHUNTER++sad is an implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing.

::DEVELOPER

Mathieu Lemire

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 GENEHUNTER++sad

:: MORE INFORMATION

Citation

Lemire M, Roslin NM, Laprise C, Hudson TJ, Morgan K (2004)
Transmission ratio distortion and allele sharing in affected sib-pairs — a new linkage statistic with reduced bias, with application to chromosome 6q25.3.
Am J Hum Genet. 75:000-000.

tRMA 1.0 – Modification of RMA to Normalize Microarray Experiments

tRMA 1.0

:: DESCRIPTION

tRMA is a modification of RMA to normalize microarray experiments for correlation-based analysis.

::DEVELOPER

Usadel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

  tRMA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Nov 11;11:553. doi: 10.1186/1471-2105-11-553.
Algorithm-driven artifacts in median Polish summarization of microarray data.
Giorgi FM, Bolger AM, Lohse M, Usadel B.

GENEHUNTER-IMPRINTING 2.1r3 / GENEHUNTER-MODSCORE 3.0 / GENEHUNTER-TWOLOCUS 1.3 – Modification of the GENEHUNTER

GENEHUNTER-IMPRINTING 2.1r3 / GENEHUNTER-MODSCORE 3.0 / GENEHUNTER-TWOLOCUS 1.3

:: DESCRIPTION

GENEHUNTER-IMPRINTING is a modification of the GENEHUNTER software package . It allows for a parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes – that is, of traits showing a parent-of-origin effect. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait. Therefore, a disease model which accounts for imprinting includes four penetrances instead of only three. For an analysis with a four-penetrance imprinting model, the command ‘imprinting on’ needs to be entered at the beginning of a GENEHUNTER-IMPRINTING session. Otherwise, LOD scores are calculated under a standard three-penetrance model, in the same way as with the original GENEHUNTER.

GENEHUNTER-MODSCORE is a further extension of GENEHUNTER-IMPRINTING.It can handle autosomal or pseudoautosomal loci. GENEHUNTER-MODSCORE allows for a MOD-score analysis, in which parametric LOD scores are maximized over the parameters of the trait model, i.e., the penetrances and disease allele frequency. By this means, the disease-model parameter space is explored in an efficient way, and so researchers do not have to rely on a single trait model when performing a parametric linkage analysis.

GENEHUNTER-TWOLOCUS is a modification of the GENEHUNTER software package. The program performs parametric and nonparametric multi-marker linkage analysis of dichotomous traits with two autosomal diallelic disease loci. It uses two unlinked marker maps with one disease locus linked to each map.

::DEVELOPER

Institute of Genetic Epidemiology (IGE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows

:: DOWNLOAD

 GENEHUNTER-IMPRINTING , GENEHUNTER-MODSCORE , GENEHUNTER-TWOLOCUS

:: MORE INFORMATION

Citation

Strauch K, Fimmers R, Kurz T, Deichmann KA, Wienker TF, Baur MP (2000):
Parametric and nonparametric multipoint linkage analysis with imprinting and two-locus-trait models: application to mite sensitization.
American Journal of Human Genetics 66:1945-1957.

Mattheisen M, Dietter J, Knapp M, Baur MP, Strauch K (2008):
Inferential testing for linkage with GENEHUNTER-MODSCORE: the impact of the pedigree structure on the null distribution of multipoint MOD scores.
Genetic Epidemiology 32:73-83

Dietter J, Spiegel A, an Mey D, Pflug HJ, Al-Kateb H, Hoffmann K, Wienker TF, Strauch K (2004):
Efficient two-trait-locus linkage analysis through program optimization and parallelization: application to hypercholesterolemia.
European Journal of Human Genetics 12:542-550

POSTMan 2.0a – POST-translational Modification analysis

POSTMan 2.0a

:: DESCRIPTION

POSTMan is a software application developed at PROBE in cooperation with Stix AS, designed to aid the researcher in identifying post-translationally modified peptides present in a given sample. POSTMan aligns LC-MS runs (MS1 data) and isolates pairs of peptides which differ by a user defined specific mass difference (Post-translationally modified peptides). Candidate peptides can then be targeted for fragmentation in a second round of analysis allowing the identification of low abundant post-translationally modified peptides.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  POSTMan

:: MORE INFORMATION

Citation

POSTMan (POST-translational modification analysis), a software application for PTM discovery.
Arntzen MØ, Osland CL, Raa CR, Kopperud R, Døskeland SO, Lewis AE, D’Santos CS.
Proteomics. 2009 Mar;9(5):1400-6.

mPrimer3 1.0 – Modification of Primer3

mPrimer3 1.0

:: DESCRIPTION

mPrimer3 (Modified Primer3) is a modification of Primer3

mPrimer3 Online Version

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 mPrimer3

:: MORE INFORMATION

Citation

Bioinformatics. 2007 May 15;23(10):1289-91. Epub 2007 Mar 22.
Enhancements and modifications of primer design program Primer3.
Koressaar T, Remm M.

seq-gen-cov – Modification of Seq-gen

seq-gen-cov

:: DESCRIPTION

seq-gen-cov is a modification of seq-gen. C program that simulates nucleotide sequences under a variety of models, including the covarion models.

::DEVELOPER

Cécile Ané

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/ MacOsX
  • C Compiler

:: DOWNLOAD

 seq-gen-cov

:: MORE INFORMATION