Computational protocol: Conserved Structural Domains in FoxD4L1, a Neural Forkhead Box Transcription Factor, Are Required to Repress or Activate Target Genes

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Protocol publication

[…] FoxD4/FoxD4L1 sequences were retrieved from Ensembl database 69 (ensembl.org) based on chromosome synteny and sequence homology. Accession numbers of FoxD4/FoxD4L1 sequences used in this analysis are provided in . Multiple sequence alignments were constructed using T-COFFEE, version 7.7.1. (tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi . Aligned FoxD4/FoxD4L1 proteins were edited using BioEdit Sequence Alignment Editor version 7.0.4.1. . The expectation-maximization algorithm of the MEME program (Multiple Em for Motif Elicitation, Version 4.9.0) was used to identify potential functional and regulatory motifs in the C-terminus on the server (hmeme.nbcr.net/meme/). The search parameters used were 6–8 motifs per a run and a motif size of 8–15 amino acid residues. The protein sequences of FoxD4/FoxD4L1 also were analyzed for the presence of canonical leucine zippers using server (2zip.molgen.mpg.de/) . Finally, the prediction of secondary FoxD4L1A (Xenopus laevis) structure was conducted using Psipred , , Porter and a consensus secondary structure prediction on the server: npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page = /NPSA/npsa_seccons.html. The helical wheel was modulated using the sequence FoxD4L1A (313–330 aa) on the server cti.itc.virginia.edu/∼cmg/Demo/wheel/wheelApp.html. All analyses were repeated at least 3 times. […]

Pipeline specifications

Software tools T-Coffee, BioEdit, PSIPRED
Application Protein structure analysis
Organisms Xenopus laevis
Chemicals Amino Acids, Glycine, Tryptophan, Glutamic Acid