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2017-07-11
Congratulations Philipp Fervers for for the successful defense of his doctoral thesis.
2017-07-24
Yukie Kashima, welcome to our institute!
2017-07-11
"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.
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2017-07-03
Welcome Reza Halabian, our new PhD student..
2017-06-27
"Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer” by Suzuki et al. has bee published by DNA Research.
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2017-07-14
"Serotyping dengue virus with isothermal amplification and a portable sequencer.” by Yamagishi at al. has been published by Scientific Reports.
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2017-04-21
"Contribution of Transposable Elements to Human Proteins" by Makalowski, Kischka and Makalowska has been published by eLS.
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2017-04-25
"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.
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2017-03-07
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