Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

Abstract

Spliced alignment plays a central role in the precise identification of eukaryotic gene structures. Even though many spliced alignment programs have been developed, recent rapid progress in DNA sequencing technologies demands further improvements in software tools. Benchmarking algorithms under various conditions is an indispensable task for the development of better software; however, there is a dire lack of appropriate datasets usable for benchmarking spliced alignment programs. In this study, we have constructed two types of datasets: simulated sequence datasets and actual cross-species datasets. The datasets are designed to correspond to various real situations, i.e. divergent eukaryotic species, different types of reference sequences, and the wide divergence between query and target sequences. In addition, we have developed an extended version of our program Spaln, which incorporates two additional features to the scoring scheme of the original version, and examined this extended version, Spaln2, together with the original Spaln and other representative aligners based on our benchmark datasets. Although the effects of the modifications are not individually striking, Spaln2 is consistently most accurate and reasonably fast in most practical cases, especially for plants and fungi and for increasingly divergent pairs of target and query sequences.

Draft genome of an iconic Red Sea reef fish, the blacktail butterflyfish (Chaetodon austriacus): current status and its characteristics

“…Gene models were predicted using a combined approach of homology‐based ( spaln version 2.1; Iwata & Gotoh ) and ab initio gene prediction ( augustus version 3.0.3, Stanke et al . ; glimmerhmm version 3.0.3, Kelley et al .…”

Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment

“…However, no attempt appears to have been made to examine whether the use of a profile can improve the quality of a spliced alignment, although an appreciable number of spliced alignment programs have been developed so far [27] including GeneWise [28] that supports profile-HMM-based spliced alignment. To test the effects of profiles, we used the same dataset, P491, as that used in previous studies [29,30].…”

Current methods for automated annotation of protein-coding genes

“…For example, GLEAN [44] has, according to Web Of Science, been used to annotate 41 genomes, seven of them insect genomes (four of them published since 2013), although it appeared to have inferior accuracy in the nGASP assessment [54] and the EVM paper [9]. As another example, exonerate appears to be used more often than newer spliced alignment programs with higher accuracy [8,30]. Also, large centers may favor tools that were developed in-house.…”

“…exonerate [29], Spaln [30 ], ProSplign [31]) or a representation of a protein family Approaches to predict coding genes (dark blue). RNA-Seq can be de novo assembled to transcripts (A, e.g.…”

“…The decrease is faster for methods that rely mostly on the alignment (exonerate, ProSplign) than for methods that use statistical models on gene structures, such as ab initio gene finders [30 ,33]. Iwata and Gotoh report in their assessment much better results for Spaln than for the two very often cited tools exonerate and GeneWise, in particular for more distant species pairs [30 ].…”