Computational protocol: Integrative characterization of germ cell-specific genes from mouse spermatocyte UniGene library

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Protocol publication

[…] The 24 cDNA sequences were translated into the corresponding peptide sequences, which were analyzed with the diverse computational bioinformatics tools, UCSC [] and Ensembl [], to determine intron-exon structures, chromosomal locations, and identify matches with the human chromosomal sequences. Using several computational bioinformatics tools, amino acid sequences deduced from the cDNA sequences of genes were analyzed. PSORT II [] was applied to predict protein sorting signals, cleavage sites, and intracellular localization. To predict the existence of motifs or domains in translated peptide sequences of genes, CDD [], Interproscan [] and PPSearch [] were employed. SignalP and TMHMM [] were used to determine the presence of putative signal peptides and transmembrane regions. Goblet [] was applied to predict gene ontology based on three main classes, specifically, molecular function, biological process and cellular components. […]

Pipeline specifications

Software tools PSORT, InterProScan, SignalP, TMHMM
Applications Protein sequence analysis, Membrane protein analysis
Organisms Mus musculus