Computational protocol: Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression

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Protocol publication

[…] BLAST searches were used to identify candidate orthologs in the following predicted proteomes: T. congolense, T. vivax, T. brucei gambiense, T.grayii, T. cruzi, L. major, L. braziliensis, L. mexicana, L. infantum and Bodo saltans were from geneDB (www.genedb.org/Homepage) and TriTrypDB (http://tritrypdb.org/tritrypdb/) while Phytomonas serpens data were from (). Access to pre-publication predicted proteome data for T. borreli, T. carassii, T. theileri and Euglena gracilis was kindly provided by Steve Kelly (Oxford) or was from in house sequence data. The NCBI non-redundant protein database was used for searches in other eukaryotes.JPred (http://www.compbio.dundee.ac.uk/jpred/index.html), COILS (), InterProScan (https://www.ebi.ac.uk/interpro/search/sequence-search), MotifScan (http://myhits.isb-sib.ch/cgi-bin/motif_scan), Phyre 2 (), cNLS Mapper () were used to predict domains and secondary structure and phosphorylation sites were predicted using Predict Protein (). Peptide sequences were analyzed for identity and similarity using SIAS (http://imed.med.ucm.es/Tools/sias.html). Phylogenetic trees were created using both PhyML () and MrBayes v3.2.1 () using multiple sequence alignments generated with Merge Align (). ProtTest version 2.4 () was used to determine the lset rates parameters for MrBayes analyses and the substitution model and gamma parameter for PhyML analyses. […]

Pipeline specifications

Software tools JPred, InterProScan, MyHits, Phyre, cNLS Mapper, SIAS, PhyML, MrBayes, ProtTest
Databases TriTrypDB GeneDB
Applications Phylogenetics, Protein sequence analysis
Organisms Trypanosoma brucei