SeqSimPresenter

If you prefer correct German to broken English: Es gibt eine deutsche Version der SeqSimPresenter-Information.
Version 1.0.2: Should work with Hypercard 2.3.
The number of sequenced genes and deduced gene products is increasing explosively due to the many genome sequencing projects. Hints about a function can often be derived from similarities to proteins with known function, and sequences can be grouped into families and superfamilies. For the estimation of a phylogenetic relationship, an overview of the distribution of highly conserved and less conserved regions conveys far more information than a simple number "% identity". However, it is difficult to survey this distribution for longer sequence alignments if they are displayed as usual:
SCORES     Init1: 322 Initn: 332 Opt: 532     35.8% identity in 293 aa overlap
330 340 350 360 370 380
cdc48.seq --DKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGI
:|::: :|:: :||: :||::::::| ||||||| : :|||| | ||:||:::: :
a34832 DSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLDRKIEFPM
270 280 290 300 310 320
390 400 410 420 430 440
cdc48.seq PDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLID
|::::| :::||:::|::: ||: |:|| |::: ||: ::| ||:| | :: ::
a34832 PNEEARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGM--IALARGATE
330 340 350 360 370
The SeqSimPresenter converts aligned sequences into bars of varying gray values, the local degree of black indicated the sequence similarity. The distribution of conserved sequences can be seen at a glance, making it the display of choice for the presentation of sequence comparisions in a lecture.

Hints for use

The program has multiple options to optimize the conversion of sequences to gray bars. Besides evaluating only amino acid identities, the conversion can be based on different scales of similarity (PAM, Blosum ..., even self-defined tables). Gray values are calculated by summation of the comparision results of several adjacent residues, the number of residues per summation and the shift between summations can be chosen, influencing the "smoothness" of the display. Segments of the gray bar can be marked, useful to indicate the position of a domaine of known function (e.g. ATP binding consensus). Background "noise" (even totally unrelated sequences have some identical residues) can be suppressed by specification of a threshold value. A scale bar of gray values displaying the threshold values can be included, as well as a scale of amino acid residues on the top bar. The resulting graphics are Postscript files in Adobe Illustrator format. It can be printed from the stack on a Postscript capable printer, or be displayed and further edited with Illustrator.

A description of the SeqSimPresenter has been published: Kai-Uwe Fr?hlich: Sequence Similarity Presenter: a tool for the graphic display of similarities of long sequences for use in presentations. Comput. Appl. Biosci. 10, 179-183 (1994)

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Last edited: March 6, 1997 by KaiFr