DNASTAT: a Pascal unit for the statistical analysis of DNA and protein sequences

Kleffe, J.; Hermann, Klaus; Gunia, Wilfried; Vahrson, Wolfgang; Wittig, Burghardt

doi:10.1093/bioinformatics/11.4.449

Cited by 2 publications

(2 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Many computer programs are available to obtain such parameter estimates numerically, e.g., by application of the Newton-Raphson algorithm (20,21). We used corresponding functions from StatUnit by Tue Tjur (22) as implemented in our freely distributed DNASTAT package (23). Convergence was always achieved after a few steps, but the calculations were lengthy due to the large number of observations and parameters.…”

Section: Logitlinear Models For Splice Site Recognitionmentioning

confidence: 99%

Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences

Kleffe

Hermann

Vahrson

et al. 1996

Nucleic Acids Research

View full text Add to dashboard Cite

Pre-mRNA splicing in plants, while generally similar to the processes in vertebrates and yeast, is thought to involve plant specific cis-acting elements. Both monocot and dicot introns are typically strongly enriched in U nucleotides, and AU- or U-rich segments are thought to be involved in intron recognition, splice site selection, and splicing efficiency. We have applied logitlinear models to find optimal combinations of splice site variables for the purpose of separating true splice sites from a large excess of potential sites. It is shown that plant splice site prediction from sequence inspection is greatly improved when compositional contrast between exons and introns is considered in addition to degree of matching to the splice site consensus (signal quality). The best model involves subclassification of splice sites according to the identity of the base immediately upstream of the GU and AG signals and gives substantial performance gains compared with conventional profile methods.

show abstract

Section: Logitlinear Models For Splice Site Recognitionmentioning

confidence: 99%

Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences

Kleffe

Hermann

Vahrson

et al. 1996

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Such database is like a dictionary in which each key is the name of the EST (the header of each Fasta sequence) and the corresponding value is the nucleotide sequence. When the number of ESTs is large, the program makes use of the C library DNA_Stat [ 33 ] through the ctypes python module (embedded in python version 2.5 and higher). The DNA_Stat library is currently part of the ClustDB software by Kleffe et al [ 27 ], one the fastest programs to identify groups of similar nucleotide sequences by suffix trees.…”

Section: Methodsmentioning

confidence: 99%

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data

2009

View full text Add to dashboard Cite

Background: ESTs and full-length cDNAs represent an invaluable source of evidence for inferring reliable gene structures and discovering potential alternative splicing events. In newly sequenced genomes, these tasks may not be practicable owing to the lack of appropriate training sets. However, when expression data are available, they can be used to build EST clusters related to specific genomic transcribed loci. Common strategies recently employed to this end are based on sequence similarity between transcripts and can lead, in specific conditions, to inconsistent and erroneous clustering. In order to improve the cluster building and facilitate all downstream annotation analyses, we developed a simple genome-based methodology to generate gene-oriented clusters of ESTs when a genomic sequence and a pool of related expressed sequences are provided. Our procedure has been implemented in the software EasyCluster and takes into account the spliced nature of ESTs after an ad hoc genomic mapping.

show abstract

DNASTAT: a Pascal unit for the statistical analysis of DNA and protein sequences

Cited by 2 publications

References 0 publications

Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences

Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data

Contact Info

Product

Resources

About