- Open Access
OrthoInspector: comprehensive orthology analysis and visual exploration
© Linard et al; licensee BioMed Central Ltd. 2011
- Received: 3 June 2010
- Accepted: 10 January 2011
- Published: 10 January 2011
The accurate determination of orthology and inparalogy relationships is essential for comparative sequence analysis, functional gene annotation and evolutionary studies. Various methods have been developed based on either simple blast all-versus-all pairwise comparisons and/or time-consuming phylogenetic tree analyses.
We have developed OrthoInspector, a new software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. In comparisons with existing methods, OrthoInspector improves detection sensitivity, with a minimal loss of specificity. In addition, several visualization tools have been developed to facilitate in-depth studies based on these predictions. The software has been used to study the orthology/in-paralogy relationships for a large set of 940,855 protein sequences from 59 different eukaryotic species.
OrthoInspector is a new software system for orthology/paralogy analysis. It is made available as an independent software suite that can be downloaded and installed for local use. Command line querying facilitates the integration of the software in high throughput processing pipelines and a graphical interface provides easy, intuitive access to results for the non-expert.
New sequencing technologies are dramatically increasing the number of predicted protein sequences available for high throughput comparative analyses, functional annotation or evolutionary studies. All these studies involve a transfer of information between organisms and homology is one of the most popular concepts used to address this problem. In particular, the studies rely on an accurate determination of orthology and paralogy relationships. According to the seminal definition of Fitch , orthologs are homologous genes that diverged from a single ancestral gene in their most recent common ancestor via a speciation event, whereas paralogs are homologs resulting from gene duplications. The distinction between orthologs and paralogs refers exclusively to the evolutionary history of genes and does not have functional implications stricto sensu. However, from an operational point of view, it is widely accepted that two orthologs generally share the same function . In contrast, paralogs are generally considered more divergent as new functions can emerge as the result of mutations or domain recombinations. Nevertheless, the multiplication of available genomes has underlined the necessity to distinguish two subtypes of paralogs: inparalogs and outparalogs . Inparalogs are produced by duplication(s) subsequent to a given speciation event, while outparalogs result from an ancestral duplication (relative to the given speciation event). In other words, in-paralogy and out-paralogy are concepts relative to the species under comparison. The distinction is crucial in evolutionary studies since sets of inparalogs derive from orthologs by lineage-specific expansions and thus can be considered to be co-orthologs, while outparalogs do not have orthologous relationships at all.
Today, the most commonly used approach for the prediction of homology relationships between genes and proteins (and thus orthology and paralogy relationships) involves some kind of similarity measure, which can be linked to different types of data, such as sequences, domains or even 3 D structures. In principle, phylogenetic tree-based inference represents the most accurate way to determine orthology and paralogy [3–5]. However, its use at the complete proteome scale is computationally expensive and, given the rate at which new genomes are now being sequenced, cannot be considered as a viable option for most laboratories at the present time. As a consequence, alternative algorithms based on graphs or on a combination of tree and graph representations , have been developed to infer homology relationships. Most of them involve protein Blast all-versus-all searches and use pairwise distance calculations , 3-way best-hits [8–10] or clustering-based approaches [11–13]. In general, comparative studies [14, 15] have shown that phylogenetic reconstructions have higher sensitivity and lower specificity than graph-based methods, particularly for distant organisms. Nevertheless, these methods provide good results for both sensitivity and specificity with some datasets [16, 17]. However, each of the methods has advantages and disadvantages, and the most appropriate method will depend on the user's purpose [6, 18]. Apart from the detection accuracy, other factors need to be taken into account, for example the availability and ease-of-use of the programs. Most of the methods commonly used today are made available as public software binaries and data browsing for the non-specialist is limited to web interfaces that allow remote querying of pre-calculated databases. For the more computer literate, large-scale queries can be performed and results can be retrieved in the form of flat files, although this requires a certain level of programming expertise to parse the data. To address this problem, some efforts have been made to facilitate the querying of data through presence/absence constraints and to provide global views of results via phylum-related tables . Nevertheless, the tools are still available as web-based interfaces and cannot be retrieved locally to support or maintain in-house databases.
Here we describe OrthoInspector, a new software system incorporating an original algorithm for the rapid detection of orthology and in-paralogy relationships between different species. In comparisons with existing methods, it improves detection sensitivity, with a minimal loss of specificity. Moreover, OrthoInspector has a modular design and is provided as an independent software suite that can be downloaded and installed for local use. Command line querying facilities have been developed to allow fast information selection for high throughput studies and to facilitate the integration of the software in other packages or processing pipelines. An enhanced graphical interface is designed to automate the complete software installation and data generation process for non-specialists. Finally, different visualization tools have been designed specifically to allow the in-depth exploration of the complex inter-species orthology/in-paralogy relationships detected.
Command-line and graphical versions can be used to perform Blast all-versus-all sequence searches and to generate a database containing the search results. Currently, the package is designed to allow the use of both raw and tabbed outputs produced by the classical NCBI Blast package and the recent NCBI blast+ package . Other Blast data formats can be easily added with the help of the Blast parser interface included in the package. OrthoInspector proposes options (i) to directly fill the database with the produced data or (ii) to create intermediate data dumps allowing a considerable speed-up. Sql scripts to use these dumps in mySQL and postgresSQL engines are provided in the OrthoInspector website.
After database installation, the command-line version allows fast information retrieval for high throughput studies and the use of the software in other packages. Textual queries (accession numbers, description...), batch queries (Fasta sequences in a file) or queries defining presence/absence of an ortholog in specific organisms can be performed. Both command-line and graphical versions allow the user to export data in FASTA, CSV and XML formats. New output formats can be easily coded with the help of the output interface provided.
The graphical version facilitates data querying for non-specialists. In addition, it provides a set of useful tools to retrieve clusters of orthologs covering multiple species, to produce comparative genomics results and to visualize the data.
The whole software suite is available at http://lbgi.igbmc.fr/orthoinspector. Furthermore this website contains tutorials and database dumps for test purposes.
The OrthoInspector algorithm is divided into three main steps. First, the results of a Blast all-versus-all (proteomes are blasted against each other) is provided by the user and is parsed to find all the Blast best hits for each protein and to create the groups of inparalogs. Second, the inparalog groups for each organism are compared in a pairwise fashion to define potential orthologs and/or in-paralogs. Third, best hits that contradict the potential orthology between entities are detected.
Inparalog group formation and validation
Pairwise comparison of inparalog groups
Detection of contradicting information
The third step in the algorithm is the detection of best hits that contradict the potential orthology relationships defined above. In particular, given two inparalog groups that are potentially orthologous, it is possible to find a best hit from a protein in one of the compared groups to another protein that does not belong to either of the groups. In this case, it is possible that the protein does not belong to the inparalog group. Such contradictions are highlighted by OrthoInspector with a warning signal in the algorithm output: a "red signal" indicates contradictions involving a reciprocal best hit and an "orange signal" indicates contradictions involving a simple best hit. Such signals help the user to discriminate proteins in complex inparalog groups formed by closely related sequences or in cases where the proteome of one of the compared organisms is incomplete and disturbs the precedent formation of validated inparalog groups.
Large-scale proteome analysis
We used the OrthoInspector software to study 59 organisms with approximately complete proteomes covering the main eukaryotic phyla in Protists, Fungi, Plants and Animals. We l incomplete and low coverage genomes to avoid predictions of false gene loss and artefacts in gene duplication inference . The complete list of the 59 studied organisms with their taxonomic identifiers and the number of retained protein transcripts can be found in additional file 1. For 22 higher eukaryotes, protein sequence datasets from Ensembl 56  were used. To avoid multiple transcript issues, the longest protein sequence was selected for each Ensembl-predicted gene annotated as 'protein-coding'. For example, the proteomes of Homo sapiens (22384 transcripts), Mus musculus (23117 transcripts), Xenopus tropicalis (18023 transcripts), Ciona intestinalis (14180 transcripts), Arabidopsis thaliana (31280 transcripts) or Oryza sativa japonica (57995 transcripts) were obtained from Ensembl. For eukaryotes not stored in Ensembl, the NCBI RefseqP  and Uniprot (Swissprot+TrEMBL)  databases were used. Data from both sources were retrieved using ICARUS scripts on a local SRS server  to select sequences according to their taxonomic identifiers. To remove redundant sequences, each sequence was compared to all others from the same organism using Blast. For sequences sharing more than 99% identity, manually-annotated entries from Swissprot were preferred over TrEMBL and RefseqP entries, otherwise the longest sequence was retained. Proteomes built with this protocol include Plasmodium falciparum (5234 transcripts), Trypanosoma brucei (8928 transcripts), Ostreococcus tauri (7974 transcripts), Encephalitozoon cuniculi (1903 transcripts), Emericella nidulans (9732 transcripts), Saccharomyces cerevisiae (6771 transcripts), Laccaria bicolor (17698 transcripts), Caenorhabditis elegans (22614 transcripts), Ixodes scapularis (21009 transcripts) and Drosophila melanogaster (22430 transcripts). Regardless of the source sequence database, sequences with less than 20 amino acids or more than 10000 amino acids were excluded. Finally, we obtained a pool of 940855 protein sequences.
The new NCBI-Blast+ package was then used to perform Blast all-versus-all searches between the proteomes of the 59 organisms, representing 940855 individual Blast searches in a database of 940855 sequences. Sequences were selected with an E-value cutoff of 1e-9. The searches were executed on the Décrypthon grid resources .
As expected, large-scale proteomes, e.g. in plants (green color in Figure 4), or genome-wide duplications, e.g. in fishes (medium blue), result in an increase in the number of predicted inparalog groups, whereas smaller eukaryote proteomes have relatively few groups. The number of inparalog groups is generally correlated with the proteome size and the phylogenetic distance between organisms, for instance, amniota (dark blue) have a relatively stable number of inparalog groups. Nevertheless, some exceptions can be observed. Despite having the largest proteome in the plant phylum, Oryza sativa has fewer groups than Vitis vinifera or Arabidopsis thaliana and sequences from Oryza sativa are included in relatively few inparalog groups. Further investigation showed that many sequences of this organism had a relatively small number of Blast hits to other organisms compared to other plants (data not shown). This may be partly due to some overprediction of genes in the Oryza sativa proteome, with several protein fragments or pseudogenes predicted as "protein-coding".
Another interesting observation is that all parasitic organisms generate a small number of inparalog groups compared to the other members of their phylum. In arthropods, Ixodes scapularis (deer tick) and Pediculus humanus (body louse) have less inparalog groups than Anopheles gambiae and Drosophilia melanogaster. In fungi, Encephalitozoon cuniculi, Nosema ceranae and Ustilago maydis have less inparalog groups than other members of this phylum. Lacarria bicolor is another fungus with few inparalogs, although this may be linked to its ectomycorrhizal symbiotic relationship with plant roots.
Unlike parasites or symbionts, some isolated organisms have a relatively large number of inparalog groups. For example, Strogylocentrotus purpuratus has numerous inparalog groups but is currently the only echinodermata genome available, and it is impossible to determine whether this is a characteristic of this phylum. Entamoeba histolytica has a number of inparalog groups similar to that to other organisms with the same proteome size, but individual sequences are included in more inparalog groups compared to other organisms. This might be explained by the lower quality of the proteome and/or the presence of numerous repeats, resulting in multiple Blast hits in all studied species.
Example test case: myotubularin family
Inparanoid is based on RBH and finds inparalogs having a similarity score equal to or superior to the similarity S defined by the RBH. In the fly/yeast comparison, the three fly myotubularins are more similar to each other than to the yeast myotubularin, thus they are considered as inparalogs. In the human/yeast comparison case, 6 out of 8 human myotubularins have a higher similarity score than the similarity score defined by the yeast/human RBH, but 2 proteins have lower scores and are thus not considered as inparalogs (false negatives).
The OrthoMCL algorithm begins with the same steps of RBH detection and identification of sequences within the same genome that are more similar to each other than to any sequence from another genome. Then, a graph is constructed, where nodes represent proteins and edges represent the relations, and a Markov clustering is performed. In this example, three clusters are found, with only one fly and three human myotubularins considered to be co-orthologs of the yeast myotubularin.
OrthoInspector does not consider RBHs as a preliminary condition to detect potential inparalogs, instead inparalog groups are inferred directly in each organism. For example, the three fly and eight human myotubularins are identified as inparalogs with respect to yeast. In a second stage, the pairwise comparison of inparalog groups exploits the RBH and BH found between the different organisms to infer many-to-one relations including all the myotubularins.
Comparison with existing methods: benchmark data sets
The accuracy of the OrthoInspector predictions was compared to five existing methods, covering the main approaches to infer orthology: namely, Inparanoid (pairwise distance comparisons), eggNOG (3-way best hits), OrthoMCL and OMA (graph clustering) and Ensembl compara (phylogenetic tree inference). Today, these methods are widely used by the community and their databases are cross-referenced in public databases like Uniprot. OrthoInspector is based on a pairwise distance based algorithm which makes it similar to the Inparanoid algorithm in some aspects. However, Inparanoid is directly based on reciprocal best hits (RBH) to find orthologs and inparalogs, as illustrated by the example test case described above. The first step of our algorithm identifies potential inparalog groups independently of RBH, thus exploring a larger search space for the discovery of potential orthology relations. The second step of our algorithm then compares inparalog groups that are not necessarily linked by a RBH between two organisms.
In order to compare the predictions made by OrthoInspector with the existing methods in a large scale study, we used two benchmarks from the literature [32, 33], representing varied protein families (nuclear receptors, hox families, membrane receptors...). The literature benchmarks cover many organisms, including H. sapiens, M. musculus, G. gallus, D. rerio, D. melanogaster, C. elegans and S. cerevisiae. In addition, we created our own benchmark, performing a detailed study of protein kinase families with complex evolutionary histories that represent a significant challenge for the accurate detection of orthology/paralog relationships. Protein kinases represent an ideal test case for our purposes, since they have been intensively studied and their family relationships are generally known. In fact, protein kinases have been classified into a number of groups sharing broad functional properties, based on sequence similarity in their catalytic domains, the presence of accessory domains and known modes of regulation. Using the standard classification, available at http://kinase.com/kinbase, and by studying the literature, we defined a test set of well annotated protein kinase sequences, from the CMGC group (including cyclin-dependent kinases, mitogen-activated protein kinases, glycogen synthase kinases and CDK-like kinases) and from the TKL (tyrosine kinase-like) group. CMGC kinases represent a homogeneous group, where most proteins possess only the kinase catalytic domain. In contrast, the TKL kinases are more divergent, often having additional domains that regulate kinase activity, link to other signaling modules, or localize the protein in the cell. The CMGC and TKL groups can be further sub-divided into several protein families. The distribution of these families was established by a combination of published in silico and wet-lab studies in a number of model organisms, including D. discoideum, C. elegans, S. cerevisiae, D. melanogaster, M. musculus and H. sapiens. Our test set consisted of 329 manually annotated sequences from these six organisms, covering 31 CMGC sub-families and 16 TKL sub-families (additional file 4).
Taken individually, the four benchmarks highlighted some contrasting results. For example, OMA obtained a sensitivity <50% for both TKL and CMGC benchmarks, compared to >60% for all other methods. This was due to the fact that OMA failed to predict some orthology relations existing between distant organisms (e.g. human and C. elegans, S. cerevisiae or D. discoideum). Ensembl compara had higher sensitivity than OrthoInspector for both kinase benchmarks (TKL:+1%, CMGC:+6%) and OrthoMCL had higher sensitivity for the CMGC kinases (+2%), but not TKL kinases (-8%). In the case of the literature benchmark n°1, all methods achieved a good sensitivity and a good specificity, which was not unexpected since the benchmark contains essentially human/mouse and human/worm relations. For the literature benchmark n°2, the results were more variable. OrthoMCL and eggNOG had high sensitivity (> 90%), but their specificity was surprisingly low (< 40%). In this benchmark, some protein families (heat shock proteins, collagens...) are totally included in a few or a single cluster. This observation is particularly true in the case of distant organism comparisons (human versus C. elegans, S. cerevisiae...).
It is clear from these results that the different methods tested here provide complementary approaches for orthology inference. In the future, it should be possible to combine the advantages of the alternative methods to improve both sensitivity and specificity. For example, OrthoInspector could be used as a starting tool to infer orthology relations, since its sensitivity and specificity are well balanced compared to most of the other methods tested here. Furthermore, the orthology inference is less computationally intensive than Ensembl compara, the only other method that achieved similar results. In a subsequent refinement step, the user could then integrate information about true/false positives from lower specificity methods such as eggNOG, OrthoMCL or Ensembl compara and lower sensitivity methods like Inparanoid or OMA methods.
Data management and visualization
The main goal of the OrthoInspector project was to build a complete software suite for orthology and inparalogy prediction and analysis. Nevertheless, in the face of the huge amounts of data being produced by the new sequence technologies, it was clearly crucial to incorporate efficient data management and update procedures in the design of the software. Thus, the complete construction of a database of orthologs can be managed via a four step user-friendly process. OrthoInspector provides administrator tools, accessible via a command-line or a graphical interface, that take as input: (i) the results of a Blast all-versus-all search in a specified directory, (ii) the fasta proteomes of the organisms used in the Blast searches together, with an XML format file describing the organisms (name, source, taxonomic identifier...). The administrator can then launch the installation procedures that will automatically fill a database with all the required information and calculated data. Subsequent updates of the database are facilitated by the architecture of the database. For example, new proteomes can be added by updating the previously mentioned input data. In contrast to other available systems, after installation the pre-calculated data can be exploited via both command-line and graphical interfaces.
The command-line client interface is designed to allow fast information retrieval for high throughput studies. It also facilitates the incorporation of the software in other packages or processing pipelines. The client provides database querying facilities via a number of different methods: textual searches allow access to results via sequence accession numbers or sequence descriptions, while batch queries permit submission of multiple Fasta-formated sequences. In addition, constraints of presence/absence of orthologs in specified organisms can be defined. Data can be exported in CSV, FASTA or XML formats. New user-defined file formats can easily be added to the software using a java interface included in the source code.
Various methods have been developed previously to predict the orthology/inparalogy relationships existing between different proteomes. In most cases, the algorithms are made publicly available in the form of binary programs that can generate either simple databases or flat files containing the complete set of predicted relationships. Until now, no comprehensive set of tools has been provided to process, query and update the datasets easily and efficiently. For this reason, we have developed OrthoInspector, incorporating fast and easy-to-use data management tools, as well as a novel algorithm to produce fast and sensitive predictions of orthology/inparalogy. The software suite, portable to any Java-compatible system and easily integrated in any workflow application, is suitable for use in high-throughput studies, which are becoming more and more predominant in the era of systems biology. Its fast and user-friendly procedures facilitate the production of databases adapted to the user's needs. It also supports more detailed analyses of interesting orthology relationships for non-specialists, who can exploit the generated databases in a graphical interface that provides novel visualization capabilities and comparative genomics tools.
In the future, OrthoInspector will be enhanced to further improve the database update process. Although tools are currently provided to easily incorporate new genomes selected by the user, keeping up with the rate of next generation sequencing will be a major challenge. The most time-consuming step in all orthology prediction algorithms is the generation of the Blast all-versus-all searches for each new update. In spite of the efforts aimed at developing faster parallelized Blast methods [40, 41], the Blast all-versus-all computational requirements grow quadratically with the addition of new proteomes. Therefore, one of our future goals will be to develop an incremental update process, minimizing the number of distance calculations required between the thousands of sequences present in the previous version of the database. We also plan to enrich the OrthoInspector system by incorporating functional annotations, such as Gene Ontology terms  or links to the Interpro protein domain database , facilitating integrated systems biology studies. Finally, to improve the interoperability of OrthoInspector with other software packages, the Ortho-XML format http://orthoxml.org will be included in the next release of OrthoInspector.
Availability and Requirements
Project name: OrthoInspector
Project home page: http://lbgi.igbmc.fr/orthoinspector/
Operating system: cross-platform
Programming language: Java
Requirements: Java JVM 1.6.x
License: GNU GPL version 3
We would like to thank Jean Muller for many fruitful discussions, Hoan N'guyen, Nicodème Paul and Raymond Ripp for help with programming and database development and the members of the Strasbourg Bioinformatics Platform (BIPS) for their support. The work was developed within the framework of the Decrypthon program, co-funded by Association Française contre les Myopathies (AFM), IBM and Centre National de la Recherche Scientifique (CNRS). We acknowledge financial support from the ANR (EvolHHuPro: BLAN07-1-198915 and Puzzle-Fit: 09-PIRI-0018-02) and Institute funds from the CNRS, INSERM, and the Université de Strasbourg.
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