Computational protocol: Unraveling flp-11/flp-32 dichotomy in nematodes

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Protocol publication

[…] A reciprocal Basic Local Alignment Search Tool (BLAST) based approach was employed to identify flp-11 and -32 sequelogs within publically available nematode genomic and transcriptomic datasets. This included species from clades 2, 4, 8, 9, 10 and 12 (). The BLAST analysis was conducted between July 2013 and May 2015; BLAST servers employed and databases queried are outlined in . Prepropeptide and protein sequences for C. elegans flp-11 and -32 were used as search strings in translated nucleotide (tBLASTn) and protein (BLASTp) BLAST analyses of available datasets. Predicted FLP-11 and -32 prepropeptide sequelogs were aligned using the Vector NTI Advance™11 AlignX® multiple sequence alignment tool (), using default settings. Prepropeptide cleavage sites were identified using previously described prediction methods (). Putative flp-11 splice sites were identified by examination of the intron/exon boundaries (where adequate genomic information was available) associated with known C. elegans and P. redivivus flp-11 splice variants. flp-11 and -32 putative N-terminal secretory signal peptides were identified using SignalP 4.1 (). […]

Pipeline specifications

Software tools BLASTN, TBLASTN, BLASTP, Vector NTI Advance, SignalP
Applications Protein sequence analysis, Amino acid sequence alignment
Organisms Caenorhabditis elegans
Chemicals FMRFamide