University School of Medicine

Extended Search


Congratulations Philipp Fervers for for the successful defense of his doctoral thesis.
Yukie Kashima, welcome to our institute!
"Inferring clonal structure in HTLV-1-infected individuals: towards bridging the gap between analysis and visualization” by Farmanbar et al. has bee published by Human Genomics.
Welcome Reza Halabian, our new PhD student..
"Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer” by Suzuki et al. has bee published by DNA Research.
"Serotyping dengue virus with isothermal amplification and a portable sequencer.” by Yamagishi at al. has been published by Scientific Reports.
"Contribution of Transposable Elements to Human Proteins" by Makalowski, Kischka and Makalowska has been published by eLS.
"Multicolor immuno- fluorescence reveals that p63- and or K5-positive progenitor cells contribute to normal breast epithelium and usual ductal hyperplasia but not to low-grade intraepithelial neoplasia of the breast." by Boecker / Korsching et al. has been published by Virchows Archiv.
Congratulations to Marcin Jakalski for the successful defense of his PhD thesis.

Gene Prediction and Feature Finding

  • Mesquite: A modular system for evolutionary analysis
  • Genscan D + M -- identification of complete gene structures in genomic DNA
  • GenomeScan -- predicts genes incorporating protein homology
  • RGD -- comparative mapping tool for rat-mouse-humany synteny
  • FGENEH -- splice sites, coding exons, gene models, promotor and polyA
  • Softberry -- nucleotide sequence analysis, genes, promoters
  • TwinScan -- gene prediction for eukaryotic genomic sequences
  • WebGene -- ten tools for analysis of protein-coding gene structure
  • Rosetta -- predicts human coding exons based on homology
  • GrailEXP -- exons, genes, promoters, polyA, CpG islands at ORNL
  • GeneWise2 -- compares protein to genomic with introns and frameshifts
  • Genie -- finds multi-exon genes only, trained on human
  • AAT -- analysis and annotation tool for finding genes
  • HMMgene -- prediction of vertebrate and nematode genes
  • NetGene2 -- neural network predictions of splice sites
  • GeneMark -- gene prediction server at EBI
  • GeneID -- gene prediction of selected signals and exons
  • RNAGenie -- locates RNA genes from secondary structures
  • Vienna RNA -- seven RNA analysis tools
  • Reverse Comp -- reverse complement of DNA sequence
  • McPromoter -- finds eukaryotic RNA polymerase II transcription starts
  • PromoterScan -- predicts promoters using homologies with Pol II promoters
  • ORF Finder -- open reading frame finder for ORFs of cutoff size
  • SeqTrans -- identifies open reading frames in finished genomic
  • Emboss -- predict CpG islands and isochores
  • UTR -- untranslated regions of eukaryotic mRNAs
  • AltSplice -- database of alternate splicing in Ests and disease genes
  • Webcutter -- finds restriction endonuclease sites
  • FSED -- frameshift error detection in new sequences
  • CheckSeq -- uses homology to find coding regions and sequence errors
  • ERR_WISE -- detection of frameshift sequencing errors
  • SEQERR -- detection of frameshift error in coding regions
  • MutCheck -- transcription and translation effect of mutations
  • Sift -- predicts tolerated and untolerated protein substitutions
  • TransFac -- transcription factor database and tool collection
  • MatInspector -- searches for transcription factor binding sites
  • VarSplice -- collection of annotated splice variants
  • TransPath -- pathways in regulation of transcription factors
  • TfScan -- scans DNA sequences for transcription factors
  • RepeatMasker -- finds retroposons and repeats
  • Censor -- finds repeated elements, Repbase updates, maps
  • Tandem -- tandem repeat finder in DNA
  • DotPlot -- dot plot for internal DNA sequence repeats
  • PatternHunter -- finds approximate repeat patterns in genomic DNA
  • TandemRepeats -- finds adjacent imperfect repeat patterns in DNA
  • Dst -- finds human repeats and separated self-homology
  • REPuter -- genomic repeats of all types to 100kbp
  • Tinoco -- suggests secondary structure in RNA or DNA
  • RNA_align -- aligns two RNA species from secondary and tertiary structures
  • REP -- searches proteins for internal repeats
  • Radar -- detects and aligns protein repeats
  • Repro -- recognises repeats in a single protein query