Posts tagged ‘EST’

• Searching for poly(A) tails - December, 2009
  sequence analysis, fasta, EST

  Poly-A tails is an inherent feature of mRNA sequences, and although they are useful to identify the end of transcripts, often we want to remove them before further analysis. Here is an algorithm to identify poly-A tails in FASTA sequences.
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• The FASTQ file format for sequences - September, 2008
  software, shell, EST

  The FASTQ format is the format of choice for most new sequencing technologies. Here, we implement a Haskell parser, and look at some ..uh, interesting properties of the format and its implementations.
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• Functional bash bracketing - July, 2008
  software, shell, EST

  My current development project is an EST pipeline. For various reasons, it is implemented in shell --- bash, to be exact. In other words, the pipeline is a script, or rather a set of scripts, that will tie together the various stages: masking, clustering, assembly, and annotation.
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