Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes

Abstract

The current cheapening of next-generation sequencing has led to an enormous growth in the number of sequenced genomes and transcriptomes, allowing wet labs to get the sequences from their organisms of study. To make the most of these data, one of the first things that should be done is the functional annotation of the protein-coding genes. But it used to be a slow and tedious step that can involve the characterization of thousands of sequences. Sma3s is an accurate computational tool for annotating proteins in an unattended way. Now, we have developed a completely new version, which includes functionalities that will be of utility for fundamental and applied science. Currently, the results provide functional categories such as biological processes, which become useful for both characterizing particular sequence datasets and comparing results from different projects. But one of the most important implemented innovations is that it has now low computational requirements, and the complete annotation of a simple proteome or transcriptome usually takes around 24 hours in a personal computer. Sma3s has been tested with a large amount of complete proteomes and transcriptomes, and it has demonstrated its potential in health science and other specific projects.

A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species Quercus ilex

“…For that reason, the Illumina Hiseq 2500 platform was employed to analyze the tissue mix sample, resulting in 119889 contigs, and 31973 Blast2GO annotated transcripts ( Guerrero-Sanchez et al, 2017 ). The number of annotated sequences have been increased to 62628 after a UniRef90 database search through Sma3s software ( Muñoz-Mérida et al, 2014 ; Casimiro-Soriguer et al, 2017 ). Among them, 27089 sequences corresponded to unique genes.…”

“…Assembled sequences were blasted against UniRef90 (UniProt 1 ) using the software Sma3s ( Casimiro-Soriguer et al, 2017 ) in order to obtain the annotated sequences with the most probable gene name and protein description, EC numbers for enzymes, GO terms, and UniProt keywords and pathways. In addition, their functions were identified using MERCATOR 2 .…”

Within-individual phenotypic plasticity in flowers fosters pollination niche shift

“…We used Trinotate v3 83 to annotate the 47,870 genes using the uniport_sprot and Pfam-A databases, and mapping the longest isoform of each of those genes. Additionally, we used sma3s 84 with similar results. For the gene ontology (GO) enrichment analyses, we used the Bioconductor package goseq 85 .…”

Draft Genome Sequences of Six Lactobacillus pentosus Strains Isolated from Brines of Traditionally Fermented Spanish-Style Green Table Olives

“…The genomes were assembled with Velvet 1.2.10 ( 9 ), and parameters were optimized with VelvetOptimiser 2.2.5 ( 9 ). The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) was used to annotate the six strains, and the annotation was completed by use of the following protocol: protein-coding genes were predicted using Prodigal v 2.6.3, which is an accurate prokaryotic gene finder ( 10 ), and then they were functionally annotated by Sma3s v2 using UniProt bacteria to get a higher sensitivity ( 11 ). To annotate noncoding genes, Infernal 1.1.2 ( 12 ) was used with Rfam database 13.0 ( 13 ).…”