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Author test

This is an unpublished method for distinguishing between coding and noncoding segments of a DNA sequence. It is basically an extension of the Codon Usage method in which we compare the sequence to two tables of codon usage to see which of the two it is most like. One table should contain typical codon usage from a coding sequence and the other typical codon usage from a noncoding region. It is based on methods used to decide authorship of text - is the usage of words (codons) more like that of author A (coding) or that of author B (noncoding)?

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(Click for full size image)

The results for each reading frame are plotted in the graphics window with frame 1 in the top panel, frame 2 the middle and frame 3 in the bottom panel. Frame 1 is the frame of the first base in the active region. At each position along the sequence the program also plots a single dot for the reading frame with the highest score. These dots appear at the midpoints of the three panels and will form a continuous line if one reading frame is consistently the highest scoring. The figure shows a nip plot window containing the results of the author test method on a sequence from E. coli. Also visible are the cross hairs. Their x position is shown in sequence base numbers in the left hand box above the plot, and the y coordinate, expressed using the score values of the gene search, is shown in the right hand box. Each line in the window has its own colour and can be dragged and dropped to new locations to reorganise the plot. The cursor in the plot can be used to control the position of the cursor in the sequence display.

A typical pair of concatenated codon tables for use by the Author test

      ===============================================
      F ttt     0 S tct     6 Y tat     2 C tgt     3
      F ttc     3 S tcc     8 Y tac     6 C tgc     0
      L tta     0 S tca     0 * taa     0 * tga     0
      L ttg     1 S tcg     0 * tag     0 W tgg     0
      ===============================================
      L ctt     1 P cct     0 H cat     0 R cgt    12
      L ctc     1 P ccc     0 H cac     4 R cgc     5
      L cta     1 P cca     2 Q caa     2 R cga     0
      L ctg    19 P ccg     7 Q cag    12 R cgg     0
      ===============================================
      I att     5 T act     3 N aat     2 S agt     2
      I atc    22 T acc     6 N aac     7 S agc     1
      I ata     0 T aca     1 K aaa     8 R aga     0
      M atg     8 T acg     0 K aag     2 R agg     0
      ===============================================
      V gtt    14 A gct    12 D gat     7 G ggt    16
      V gtc     1 A gcc     4 D gac     9 G ggc    11
      V gta     7 A gca     8 E gaa    14 G gga     0
      V gtg     4 A gcg     5 E gag     2 G ggg     0
      ===============================================
      ===============================================
      F ttt    16 S tct     8 Y tat     8 C tgt    12
      F ttc     7 S tcc     0 Y tac     4 C tgc     8
      L tta     7 S tca     9 * taa    14 * tga     6
      L ttg     7 S tcg     5 * tag     2 W tgg    17
      ===============================================
      L ctt     4 P cct     5 H cat     7 R cgt     4
      L ctc     1 P ccc     0 H cac     7 R cgc     8
      L cta     2 P cca     2 Q caa     3 R cga     4
      L ctg     6 P ccg     1 Q cag     7 R cgg     4
      ===============================================
      I att     5 T act     3 N aat     3 S agt     4
      I atc     2 T acc     5 N aac     1 S agc     1
      I ata     6 T aca     8 K aaa    13 R aga     7
      M atg     4 T acg     5 K aag     9 R agg     6
      ===============================================
      V gtt     5 A gct     2 D gat     3 G ggt     3
      V gtc     3 A gcc     4 D gac     3 G ggc     5
      V gta     2 A gca     4 E gaa     3 G gga     2
      V gtg     5 A gcg     5 E gag     2 G ggg     5
      ===============================================

The mathematical treatment of the data is very different from that of the codon usage method.

Given the two tables of codon usage the algorithm works out the optimal weighting to give each codon to obtain the best discrimination between coding and noncoding sequence. From this it works out the coding weighted mean and noncoding weighted mean and their variances. Then when using a fixed window length to classify a segment of sequence into coding or noncoding the probability of an error and the window length are related by: fact = sqrt ( window_length ) * S where S is the error size in standard deviations. The discriminating value d = non_wm + ( fact * sqrt ( window_length ) * non_sd where non_wm is the noncoding weighted mean and non_sd is its standard deviation. From this the algorithm calculates the window length that corresponds to an error rate of 1/1000 and uses that to scan the sequence.

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The user should supply the name of a file containing two concatenated codon usage tables - the first being from coding sequence and the second from noncoding sequence. The two tables can be calculated by nip4 and saved to disk before being concatenated. If the user gives the name of a file that contains only a single codon table the algorithm will assume that it is from coding sequence, and will generate a noncoding table that consists of the frequencies that would be expected if the sequence being analysed was random. The region to be analysed can also be set.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/nip4_24.html