Downloads
Below are a list of programs and data available from our lab
AGEseq: Analysis of Genome Editing by Sequencing
PEAL SCRIPT: AGEseq.zip
BLAT FOR WINDOWS XP, VISTA, 7: blat_windows.zip
BLAT FOR WINDOWS 10: blat_windows10.zip
A test dataset from one transgenic line: 4CL1-61_S11.txt
SLIM: A Sliding Linear Model for Estimating the Proportion of True Null Hypotheses in Datasets With Dependence Structures
CorSig: A General Framework for Estimating Statistical Significance of Correlation and Its Application to Gene Co-expression Analysis.
citation: Wang H-Q and Tsai C-J (2013) PLoS One 8(10): e77429
Populus microarray annotation
citation: Tsai C-J, Ranjan P, DiFazio SP, Tuskan GA, Johnson V (2011) Poplar genome microarrays. In: Joshi CP, DiFazio SP and Kole C (eds), Genetics, Genomics and Breeding of Poplars. Science Publishers, Enfield, NH. pp. 112-127.
Xue L-J, Guo W, Yuan Y, Anino EO, Nyamdari B, Wilson MC, Frost CJ, Chen H-Y, Babst BA, Harding SA, Tsai C-J (2013) Plant Cell 25: 2714-2730.
Xue L-J, Alabady MS, Mohebbi M, Tsai C-J (2015) Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremula x alba 717-1B4. Tree Genetics & Genomes 11: 82.
Extraction of Promoter sequences from the genome
PERL SCRIPTS & README: sut_promoter.zip
sPta717 v2 sequence and annotation files
sPta717alba_v2_gene_model.fa.gz
sPta717alba_v2_transcript.fa.gz
sPta717tremula_v2_gene.gff3.gz
sPta717tremula_v2_gene_model.fa.gz