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Amino acid sequences for human NF-H (Accession QFHUH), lamin A/C (Accession P02545), and B (Accession P20700), and human GFAP (Accession XP_050159) were obtained from the National Center for Biotechnology Information Protein Data Base http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Protein.
In some cases, manual processing of the sequences was necessary using the VecScreen program at the National Canter for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html.
This problem was also the topic of a recent meeting in Heidelberg, “Best Practice in Microarray Studies” (http://www.biometrie.uni-heidelberg.de/workshops/bestpractice/index.htm).
We use the Pfam protein family database [ 8 ] as a source of high quality curated multiple sequence alignments and profile HMMs (Hidden Markov Models, see [ 21 ] for a review), as well as programs from the HMMER package http://hmmer.wustl.edu/.
The sequences used in this study can be accessed through the NCBI website at http://www.ncbi.nih.gov, the Fugu rubripes website at http://genome.jgi-psf.org/fugu6/fugu6.home.html [ 47 ] and the FlyBase Consortium website at http://flybase.org/ [ 48 ] . The Fugu scaffold identities presented here refer to assembly v.3.