Tool:Shell Wrappers for EMBOSS utilities
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7.5 years ago

Please find shell wrappers for some of the EMBOSS utilities to make them compatable with metagenomic whole-genome shotgun contigs:

  • compseq.sh: calculate the composition of unique words in sequences
  • dan.sh: calculate nucleic acid melting temperature
  • density.sh: calculate nucleic acid density
  • cpgreport.sh: identify and report CpG-rich regions in nucleotide sequence
  • newcpgreport.sh: identify CpG islands in nucleotide sequence
  • fuzznuc.sh: search for patterns in nucleotide sequences
  • fuzztran.sh: search for patterns in protein sequences (translated)
  • freak.sh: generate residue/base frequency table
  • etandem.sh: find tandem repeats in a nucleotide sequence
  • tcode.sh: identify protein-coding regions using Fickett TESTCODE statistic
  • getorf.sh: find and extract open reading frames (ORFs)

Best Wishes,
Umer

contigs perl metagenomics emboss bash • 1.6k views
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