:: DESCRIPTION
AlgPred is a web server which has been developed for the predicting allergenic proteins and for mapping IgE epitopes on allergenic proteins
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W202-9.
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes.
Saha S1, Raghava GP.
:: DESCRIPTION
Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. Spaln adopts multi-phase heuristics that makes it possible to perform the job on a conventional personal computer running under Unix/Linux with limited memory. The program is written in C++ and distributed as source codes and also as executables for a few platforms. Unless binaries are not provided, users must compile the program on their own system. Although the program has been tested only on a Linux operating system, it is likely to be portable to most Unix systems with little or no modifications. The accessory program sortgrcd sorts the gene loci found by spaln in the order of chromosomal position and orientation.
::DEVELOPER
Computational Biology Research Center (CBRC),
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gotoh, O.
“A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence”
Nucleic Acids Research 36 (8) 2630-2638 (2008).
:: DESCRIPTION
Quantitative effects of each mutation at each position in the RNA can be recovered with statistical certainty using the herein developed user-friendly, cross-platform software MIMEAnTo (MIME Analysis Tool).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments.
Smith MR, Smyth RP, Marquet R, von Kleist M.
Bioinformatics. 2016 Jul 10. pii: btw479.
:: DESCRIPTION
SeqSaw is a package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Biochem Biophys Res Commun. 2011 Jun 3;409(2):299-303. Epub 2011 May 7.
Observations on novel splice junctions from RNA sequencing data.
Wang L, Wang X, Wang X, Liang Y, Zhang X.
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:: DESCRIPTION
readaligner is a tool for mapping (short) DNA reads into reference sequences.
::DEVELOPER
Succinct Data Structures (SuDS) -research group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
V. Mäkinen, N. Välimäki, A. Laaksonen and R. Katainen:
Unified View of Backward Backtracking in Short Read Mapping.
To appear in Ukkonen Festschrift 2010 (Eds. Tapio Elomaa, Pekka Orponen, Heikki Mannila), Springer-Verlag, LNCS 6060, pp. 182-195, 2010.
:: DESCRIPTION
MASiVE (Mapping and Analysis of SIreVirus Elements) is an expertly-built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis, and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences.
::DEVELOPER
The Bioinformatics Analysis Team
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2010 Oct 1;26(19):2452-4. Epub 2010 Aug 9.
MASiVE: Mapping and Analysis of Sirevirus Elements in plant genome sequences.
Darzentas N, Bousios A, Apostolidou V, Tsaftaris AS.
:: DESCRIPTION
MMAPPR is an analysis pipeline for mapping mutations using RNA-seq. It works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hill, J. T., Demarest, B. L., Bisgrove, B. W., Gorsi, B., Su, Y.-C., & Yost, H. J. (2013).
MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq.
Genome Res. 2013 Apr;23(4):687-97.
:: DESCRIPTION
PROC QTL is a user defined SAS (Statistical analysis system) procedure for mapping quantitative trait loci (QTL).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhiqiu Hu and Shizhong Xu (2009).
PROC QTL – A SAS Procedure for Mapping Quantitative Trait Loci.
International Journal of Plant Genomics 2009: 3 doi:10.1155/2009/141234
:: DESCRIPTION
CpGpromoter is a program for a large-scale human promoter mapping using CpG islands. As defined by Gardiner-Garden & Frommer, CpG islands are greater than 200 bp in length, have more than 50% of G+C content, and have a CpG frequency of at least 0.6 of that expected on the basis of the G+C content of the region. CpG islands are an important signature of 5′ region of many mammalian genes. The program is based on results of discriminant analysis between the promoter-associated CpG islands and non-associated ones (Ioshikhes & Zhang). It enables an efficient mapping of human promoters with 2Kb resolution, if there is a CpG island inside an interval (-500…+1,500) around a transcription start site (TSS).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ioshikhes, I. & Zhang, M.Q.
Large-scale human promoter mapping using CpG islands.
Nature Genetics 26, 61-63 (2000)
