RepeatMasker RepeatScout

目录 Bioinfo
#build frequency table
build_lmer_table -sequence input_genome_sequence.fas -freq output_lmer.frequency
#create fasta file containing all kinds of repeats
RepeatScout -sequence input_genome_sequence.fas -output output_repeats.fas  -freq output_lmer.frequency
#filter out short (<50bp) sequences
filter-stage-1.prl output_repeats.fas > output_repeats.fas.filtered_1
#run RepeatMasker on your genome of interest using filtered RepeatScout library
RepeatMasker  input_genome_sequence.fas -lib output_repeats.fas.filtered_1
#filtering putative repeats by copy number
cat output_repeats.fas.filtered_1  | filter-stage-2.prl --cat=input_genome_sequence.fas.out > output_repeats.fas.filtered_2

Biosoft

目录 Bioinfo

基因组拼接:
Phrap,Soapdenovo,mira,velvet
转录组拼接:
Cufflinks,Trinity,Oases;
比对软件:
Blast,ABblast,soap,maq,bowtie,bwa
基因结构注释:
Genscan,snap,GlimmerHMM,Augustus,Fgenesh,PASA
基因功能注释:
Interproscan,KEGG,WEGO
重复序列注释:
LTR_FINDER,LTR_STRUC,Piler,Recon,RepeatModeler,RepeatSout,Trf,MISA,RepeatMasker
非编码RNA注释:
Snoscan,tRNAscan-SE,snoGPS