Related Material (II): Genome Annotation

Map Analysis in GCG: no codon frequency info required

  1. Purpose: Display open reading frames above a certain length
  2. Application: Look for orf's for further study
  3. Algorithm: Pattern search
  4. Data file required: ( Kbytes)
  5. Tips: use "-open=x" to display open reading frames longer than x amino acids long

TestCode Analysis in GCG: : no codon frequency info required

  1. Purpose: Produce a graph for determining the potential coding region
  2. Application: to determine the potential coding region
  3. Algorithm: measure of the period three constraint
  4. Data file required:

Frames Analysis in GCG: need codon frequency info

  1. Purpose: Produce a graph to display orf's and the position of rare codons
  2. Application: to determine the potential coding region
  3. Algorithm: simple translation and position display of rare codons
  4. Data file required:
  5. Tips: use "-rare" to display the position of rare codons on top of orf, use "-?" to set the definition of rara codon.

Translation Analysis in GCG

  1. Purpose:
  2. Application:
  3. Algorithm:
  4. Data file required:
  5. Tips:

Blast Analysis in GCG

  1. Purpose:
  2. Application:
  3. Algorithm:
  4. Data file required:
  5. Tips:
  6. Make sure you add "-filter=xs" filters during job submission. (You can find more information of these two filters by reading the help file for pre-processing programs shown in "2.".
  7. Pre-process the sequence before you submit the blast job using GCG's

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