Пакет: chimeraslayer (20101212+dfsg1-6)

[ Източник: microbiomeutil  ]

detects likely chimeras in PCR amplified DNA

ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500bp).

Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences:

 1. the ends of a query sequence are searched against an included
    database of reference chimera-free 16S sequences to identify potential
    parents of a chimera
 2. candidate parents of a chimera are selected as those that form a
    branched best scoring alignment to the NAST-formatted query sequence
 3. the NAST alignment of the query sequence is improved in a
    ‘chimera-aware’ profile-based NAST realignment to the selected
    reference parent sequences
 4. an evolutionary framework is used to flag query sequences found to
    exhibit greater sequence homology to an in silico chimera formed
    between any two of the selected reference parent sequences.

To run Chimera Slayer, you need NAST-formatted sequences generated by the nast-ier utility.

ChimeraSlayer is part of the microbiomeutil suite.

Етикети: Biology: Nucleic Acids, Field: Biology

Други пакети, свързани с chimeraslayer

• dep: cdbfasta

  Constant DataBase indexing and retrieval tools for multi-FASTA files

• dep: microbiomeutil-data

  Reference 16S sequences and NAST-alignments used by microbiomeutil tools

• dep: ncbi-blast+-legacy

  NCBI Blast legacy call script

• rec: nast-ier

  NAST-based DNA alignment tool

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