logo  dAtabase of Polyx Evolution

    Mier, P. & Andrade-Navarro, M. dAPE: a web server to detect homorepeats and follow their evolution. Bioinformatics, 33(2017), 1221-1223. PMID: 28031183.    

{ Mandatory → Choose between Input option A and Input option B to start the execution of dAPE. }

  dAPE helps assessing the evolution of homorepeats and their protein context. It uses by default a weak cutoff (4 out of 6 identical amino acids) to help in the identification of emerging and disappearing homorepeats.

[Input option A]  

Input one EnsemblProtein ID, UniProt AC or UniProt ID to get its polyX and their evolution using orthology data.

(Organisms in our database)

*Execution time depends solely on the query length, from one second (~500 amino acids) to around 40 seconds (~4000 amino acids).

Example 1 → one Ensembl ID (ENSP00000244769, human ataxin 1) as query. Precomputed result.
Example 2 → one UniProt AC (P42858, human huntingtin) as query. Precomputed result.

[Input option B]

Upload a file with one or more protein sequence/s, in fasta format .

or paste the sequence/s here:

*Only the first 20 sequences will be computed and examined for polyX regions.

Example 3a set of orthologous sequences as input; clustered with FastaHerder2, in one cluster.
Example 4a set of sequences from different orthologous groups as query. Clustered with FastaHerder2, in more than one cluster.

{ OptionalFilter the results, by showing only those with a minimum number of amino acid X in any of the different window lengths (WL) around each homorepeat (± 30 amino acids). By default, all polyX are shown. }

  We used by default a weak cutoff (4 out of 6 identical amino acids) to locate the homorepeats. However, you may want to filter the results to stick to longer homorepeats or to perfect ones (6 out of 6, por example). To do so, use one or more of the boxes below.
  • Example1: to get dAPE to show only perfect homorepeats of a minimum length of 8, write "8" in the window length (WL) = 8.
  • Example2: to use a cutoff of 6 out of 8 identical amino acids, write "6" in the window length (WL) = 8.
WL = 6 WL = 8 WL = 10 WL = 12 WL = 14
WL = 16 WL = 18 WL = 20 WL = 22