Reference Alignment Research Articles

Paper 208: Evaluation of Anatomical Reference for Sagittal Alignment in Total Knee Arthroplast

Paper 208: Evaluation of Anatomical Reference for Sagittal Alignment in Total Knee Arthroplast

Measurement of Femoral and Tibial Joint Reference Angles and Pelvic Limb Alignment in Cats

To report pelvic limb joint reference angles, limb alignment, and mechanical axis deviation for the feline pelvic limb. Cadaveric radiographic anatomic study. Skeletally mature, mixed breed cats (n = 50). Extended pelvic limb radiography was performed and images analyzed to determine femoral anatomic joint reference angles, femoral and tibial mechanical joint reference angles, tibiofemoral angle, metatarsotibial angle, mechanical axis-femur and mechanical axis-metatarsus angles, and mechanical axis deviation of the stifle and tarsus. Mean ± SD and 95% confidence intervals (95% CI) were calculated. Mean ± SD angles and 95% CI were: anatomic lateral proximal femoral (103.9° ± 3.8°; 103.1° - 104.6°), anatomic lateral distal femoral (93.8° ± 2.5°; 93.3° - 94.3°), mechanical lateral proximal femoral (100.5° ± 3.7°; 99.8° - 101.2°), mechanical lateral distal femoral (97.2° ± 2.2°; 96.7° - 97.6°), mechanical medial proximal tibial (88.0° ± 3.2°; 87.3° - 88.6°), mechanical medial distal tibial (107.6° ± 4.8°; 106.6° - 108.5°), mechanical tibiofemoral (7.4° varus ± 2.5°; 6.9° - 7.9°), mechanical metatarsotibial (6.0° valgus ± 3.5°; 5.3° - 6.7°); mechanical axis-femur (3.2° ± 1.4°; 2.9° - 3.5°) and mechanical axis-metatarsus (2.4° ± 2.0°; 1.7° - 2.1°). Mechanical axis deviation of the stifle and of the tarsus were 2.0% ± 0.9% (95% CI: 1.9-2.2) and 0.8% ± 1.0% (95% CI: 0.7-1.0), respectively. Mean pelvic limb joint reference and limb alignment angles can be used for diagnosing angular limb deformities of the feline pelvic limb and for planning corrective osteotomies in affected cats.

OPTIMIZING THE ROTATION AND TRANSLATION OF FINGERPRINT IMAGES USING GENETIC ALGORITHM

In the minutiae-based fingerprint authentication system, the minutiae in the query image are required to be matched with the minutiae of the reference image that is stored in the database. Ideally, the minutiae extracted from the different impressions of the same fingerprint must match with each other, but practically, because of displacement, rotation, and other linear/ nonlinear distortions, minutiae extracted from different impressions of the same fingerprint do not match with each other. In order to maximize the number of matching minutiae, the alignment of the two fingerprints is required. Correctly aligning the fingerprints requires the translation and rotation to be recovered exactly. In this article, a new genetic-algorithm (GA)-based relative alignment algorithm for the alignment of reference and query fingerprint images is proposed. With the proposed algorithm there is no need to find the reference core or delta point because reliable detection of these reference points is a difficult task. In the proposed algorithm, all the three parameters x, y (translation), and θ (rotational) have been optimized separately. In order to improve the processing time, two acceleration steps have also been implemented. The experiments conducted on the FVC2002/Db1_a database reveal that a high accuracy has been achieved with the proposed method.

Variable Reference Alignment: An Improved Peak Alignment Protocol for NMR Spectral Data with Large Intersample Variation

In an effort to address the variable correspondence problem across large sample cohorts common in metabolomic/metabonomic studies, we have developed a prealignment protocol that aims to generate spectral segments sharing a common target spectrum. Under the assumption that a single reference spectrum will not correctly represent all spectra of a data set, the goal of this approach is to perform local alignment corrections on spectral regions which share a common "most similar" spectrum. A natural beneficial outcome of this procedure is the automatic definition of spectral segments, a feature that is not common to all alignment methods. This protocol is shown to specifically improve the quality of alignment in (1)H NMR data sets exhibiting large intersample compositional variation (e.g., pH, ionic strength). As a proof-of-principle demonstration, we have utilized two recently developed alignment algorithms specific to NMR data, recursive segment-wise peak alignment and interval correlated shifting, and applied them to two data sets composed of 15 aqueous cell line extract and 20 human urine (1)H NMR profiles. Application of this protocol represents a fundamental shift from current alignment methodologies that seek to correct misalignments utilizing a single representative spectrum, with the added benefit that it can be appended to any alignment algorithm.

SAS-Pro: simultaneous residue assignment and structure superposition for protein structure alignment.

Protein structure alignment is the problem of determining an assignment between the amino-acid residues of two given proteins in a way that maximizes a measure of similarity between the two superimposed protein structures. By identifying geometric similarities, structure alignment algorithms provide critical insights into protein functional similarities. Existing structure alignment tools adopt a two-stage approach to structure alignment by decoupling and iterating between the assignment evaluation and structure superposition problems. We introduce a novel approach, SAS-Pro, which addresses the assignment evaluation and structure superposition simultaneously by formulating the alignment problem as a single bilevel optimization problem. The new formulation does not require the sequentiality constraints, thus generalizing the scope of the alignment methodology to include non-sequential protein alignments. We employ derivative-free optimization methodologies for searching for the global optimum of the highly nonlinear and non-differentiable RMSD function encountered in the proposed model. Alignments obtained with SAS-Pro have better RMSD values and larger lengths than those obtained from other alignment tools. For non-sequential alignment problems, SAS-Pro leads to alignments with high degree of similarity with known reference alignments. The source code of SAS-Pro is available for download at http://eudoxus.cheme.cmu.edu/saspro/SAS-Pro.html.

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

Despite recent progress, computational tools that identify gene fusions from next-generation whole transcriptome sequencing data are often limited in accuracy and scalability. Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency. http://bioinformatics.mdanderson.org/main/BreakFusion

ITSoneDB: a specialized ITS1 database for amplicon-based metagenomic characterization of environmental fungal communities

Motivations. Metagenomics is experiencing an explosive improvement from the advent of high-throughput next-generation sequencing (NGS) technologies which allows an unprecedented large-scale identification of microorganisms living in almost every environment. In particular, the use of amplicon-based metagenomic approach to explore the diversity of fungal environmental communities is increasingly expanding. At the species level, a number of studies have used the non-conserved internal transcribed spacers (ITS) 1 and 2 of the ribosomal RNA genes cluster as genetic markers to explore the fungal taxonomic diversity. Particularly, ITS1 is gaining an increasing popularity as better discriminating species marker in Fungi because of its higher variability compared to ITS2. Starting from the total DNA extracted from any environmental sample, this locus can be easily amplified with taxonomically universal primers and sequenced by means of high-throughput next generation platforms. Reference databases and robust supporting taxonomies are crucial in assigning phylogenetic affiliation to the huge amount of produced sequences. Even if a large number of ITS1 sequences are collected in public databases, a specialized resource focused particularly on this region, where sequences identity, boundaries and taxonomic assignment are validated, is still needed at present. In this work we present ITSoneDB, a new comprehensive collection of ITS1 sequences belonging to Fungi Kingdom. Methods. ITSoneDB has been generated and populated using a multi-step Python workflow. In the first step the ribosomal RNA gene cluster sequences of Fungi including the target ITS1 region were retrieved from Genbank. Then, ITS1 start and end boundaries were extracted from the Features Tables annotations, if available. In order to infer, validate and, eventually, redesign the ITS1 location, Hidden Markov Model (HMM) profiles of flanking genes for 18S and 5.8S ribosomal RNA, generated from their reference alignments stored in RFAM database, were mapped on the entire collection of retrieved nucleotide sequences, by means of the hmmsearch tool from HMMER 3.0 package. Results. At present, ITSoneDB includes 405,433 taxonomically arranged sequence entries provided with ITS1 both start and end positions defined by GenBank annotations and/or HMM based method. ITSoneDB front-end is a JAVA platform-based website for data browsing and downloading. The database can be queried by species or taxon name, GenBank accession ID or by "expanding" the target rank on a detailed fungal taxonomical tree. The complete ITS1 sequences dataset collected in ITSoneDB is available in Fasta format and the users can extract and locally save all or selected queried ITS1 sequences for further analysis. Availability http://itsonedb.ba.itb.cnr.it/

Three-dimensional in vivo motion analysis of normal knees employing transepicondylar axis as an evaluation parameter

The transepicondylar axis (TEA) has been used as a flexion axis of the knee and a reference of the rotational alignment of the femoral component. However, no study has showed dynamic normal knee kinematics employing TEA as the evaluation parameter throughout the full range of motion in vivo. The purpose of this study was to analyze dynamic kinematics of the normal knee through the full range of motion via the 3-dimensional to 2-dimensional registration technique employing TEA as the evaluation parameter. Dynamic motion of the right knee was analyzed in 20 healthy volunteers (10 female, 10 male; mean age 37.2 years). Knee motion was observed as subjects squatted from standing with knee fully extended to maximum flexion. The following parameters were determined: (1) Anteroposterior translations of the medial and lateral ends of the TEA; and (2) changes in the angle of the TEA on the tibial axial plane (rotation angle). The medial end of the TEA demonstrated anterior translation (3.6 ± 3.0 mm) from full extension to 30° flexion and demonstrated posterior translation (18.1 ± 3.7 mm) after 30°, while the lateral end of the TEA demonstrated consistent posterior translation (31.1 ± 7.3 mm) throughout knee flexion. All subjects exhibited femoral external rotation (16.9 ± 6.2°) relative to the tibia throughout knee flexion. Compared to previously used parameters, the TEA showed bicondylar posterior translation from early flexion phase. These results provide control data for dynamic kinematic analyses of pathologic knees in the future and will be useful in the design of total knee prostheses.

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

Motivation: Accurate alignment of large numbers of sequences is demanding and the computational burden is further increased by downstream analyses depending on these alignments. With the abundance of sequence data, an integrative approach of adding new sequences to existing alignments without their full re-computation and maintaining the relative matching of existing sequences is an attractive option. Another current challenge is the extension of reference alignments with fragmented sequences, as those coming from next-generation metagenomics, that contain relatively little information. Widely used methods for alignment extension are based on profile representation of reference sequences. These do not incorporate and use phylogenetic information and are affected by the composition of the reference alignment and the phylogenetic positions of query sequences.Results: We have developed a method for phylogeny-aware alignment of partial-order sequence graphs and apply it here to the extension of alignments with new data. Our new method, called PAGAN, infers ancestral sequences for the reference alignment and adds new sequences in their phylogenetic context, either to predefined positions or by finding the best placement for sequences of unknown origin. Unlike profile-based alternatives, PAGAN considers the phylogenetic relatedness of the sequences and is not affected by inclusion of more diverged sequences in the reference set. Our analyses show that PAGAN outperforms alternative methods for alignment extension and provides superior accuracy for both DNA and protein data, the improvement being especially large for fragmented sequences. Moreover, PAGAN-generated alignments of noisy next-generation sequencing (NGS) sequences are accurate enough for the use of RNA-seq data in evolutionary analyses.Availability: PAGAN is written in C++, licensed under the GPL and its source code is available at http://code.google.com/p/pagan-msa.Contact: ari.loytynoja@helsinki.fiSupplementary information: Supplementary data are available at Bioinformatics online.

COMPARATIVE RNA-SEQ FOR THE INVESTIGATION OF RESISTANCE TO PHYTOPHTHORA ROOT ROT IN THE RED RASPBERRY 'LATHAM'

Mechanisms of resistance to Phytophthora root rot (PRR) (caused by Phytophthora rubi) in the red raspberry (Rubus idaeus) 'Latham' were investigated with a genome-wide expression study. Root-tissues of 'Latham' (resistant to PRR) and 'Titan' (susceptible to PRR) were sampled from controls at 48 h, 5 days, and 20 days post inoculation. Total mRNA was extracted and sequencing libraries were prepared. Over 70,600,000 quality filtered 86 nt reads were sequenced with an Illumina Genome Analyzer IIx. RNA-seq was performed with these data using a freely available bioinformatics pipeline (Bowtie-TopHat and Cufflinks). The recently completed draft genome sequence of the woodland strawberry (Fragaria vesca) was used as the reference for alignment. Of 16,956 unique and putatively expressed genes detected there were 12,823 that we considered significantly expressed because the lower bound of the 95% confidence interval did not include a FPKM of zero. Furthermore, only genes that were significantly differentially expressed after Benjamini Hochberg False Discovery Rate correction for multiple testing were considered. Between the resistant control ('Latham' un-inoculated) and resistant treatment ('Latham' inoculated) 702 genes were significantly differentially expressed with a log fold change greater than 0.5 or less than -0.5 and an FPKM >3 in either the control or treatment. Further analysis was targeted toward genes known to play a role in plant defense. Significant results include: 1) increased expression of WRKY transcription factors, 2) PR genes, and 3) key genes in the citric acid cycle and the lignin biosynthetic pathways. These results are being confirmed with quantitative RT-PCR. This study not only reveals putative mechanisms of durable resistance in 'Latham', but it demonstrates how the newly released draft genome of Fragaria vesca can be used as a resource for genome-wide expression analysis in Rubus species.

Short-read, high-throughput sequencing technology for STR genotyping

DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information. High-throughput sequencing technology may provide a more powerful instrument for human identification, but is not currently validated for forensic casework. Here, we present a systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology. Open source reference alignment tools were optimized to evaluate PCR-amplified STR loci using a custom designed STR genome reference. Evaluation of this approach demonstrated that the 13 CODIS STR loci and amelogenin (AMEL) locus could be accurately called from individual and mixture samples. Sensitivity analysis showed that as few as 18,500 reads, aligned to an in silico referenced genome, were required to genotype an individual (>99% confidence) for the CODIS loci. The power of this technology was further demonstrated by identification of variant alleles containing single nucleotide polymorphisms (SNPs) and the development of quantitative measurements (reads) for resolving mixed samples.

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

BackgroundTransmembrane proteins (TMPs) constitute about 20~30% of all protein coding genes. The relative lack of experimental structure has so far made it hard to develop specific alignment methods and the current state of the art (PRALINE™) only manages to recapitulate 50% of the positions in the reference alignments available from the BAliBASE2-ref7.MethodsWe show how homology extension can be adapted and combined with a consistency based approach in order to significantly improve the multiple sequence alignment of alpha-helical TMPs. TM-Coffee is a special mode of PSI-Coffee able to efficiently align TMPs, while using a reduced reference database for homology extension.ResultsOur benchmarking on BAliBASE2-ref7 alpha-helical TMPs shows a significant improvement over the most accurate methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. We also estimated the influence of the database used for homology extension and show that highly non-redundant UniRef databases can be used to obtain similar results at a significantly reduced computational cost over full protein databases. TM-Coffee is part of the T-Coffee package, a web server is also available from http://tcoffee.crg.cat/tmcoffee and a freeware open source code can be downloaded from http://www.tcoffee.org/Packages/Stable/Latest.

High-precision laser alignment technique based on spiral phase plate

The laser alignment technique is widely used in the measurement of straightness due to its unique capabilities of non-contact detection, fast response and high accuracy. By coupling the laser beam into a single-mode fiber, traditional alignment method can be greatly improved, since the emitting beam from the fiber basically won’t be affected by the variation of the incident intensity distribution. However, such method still suffers from errors caused by the vibration of the emitting fiber end and air turbulence. In this paper, the traditional alignment reference, which is the centroid of the intensity distribution, is replaced by center of the dark spot in a diffraction pattern, by adding a spiral phase plate (SPP) into the optical path. The center of the dark spot is proved to be stationary when the laser beam drifts. The far-field diffraction model of SPP is theoretically analyzed in detail. In the calibration experiments, the detected position data of the scanned CCD is highly linear with a correlation coefficient of 0.99999. The system is guaranteed with outstanding stability by a series of experiments, in which the standard deviation of the x and y coordinates are respectively only 7.0% and 33.7% in short-term tests and 20.3% and 25.3% in long-term tests. With simple configuration, the proposed system demonstrates satisfying performance in laser alignment.

Supine Thoracolumbar Sagittal Spine Alignment

Imaging supine sagittal alignment study. Our goal was to determine differences between plain radiographs and computed tomography (CT) scans in supine sagittal alignment and to establish supine reference Cobb angles for both. Few studies have compared plain radiographs versus CT scans with regard to sagittal spine alignment. None have utilized supine patients. Fifty sequential blunt trauma individuals who had routine clearance of the thoracolumbar spine had their plain radiographs and CT scans reviewed independently by 2 spine surgeons. The Cobb method was utilized to determine angles at each spine level from T4 to L5. All imaging was obtained in the supine position, and no patient had acute ligamentous or bony pathology. Intraclass correlation coefficients (ICCs) were utilized to determine intraobserver, interobserver, and method reliability. Every level within the thoracic region was kyphotic, with a peak at T6. The lumbar region demonstrated a fairly linear progression from a near-neutral alignment at L1 to approximately 50° of lordosis at L5. The intraobserver reliability was consistent, with ICCs for Observer 1 plain radiographs at 0.653, Observer 2 plain radiographs at 0.891, Observer 1 CT scans at 0.677, and Observer 2 CT scans at 0.648. The interobserver reliability was very high, with ICCs for plain radiographs at 0.902 and 0.895 for CT scans. Finally, method reliability (between plain radiographs and CT scans) was excellent as well, with ICCs of 0.808 for Observer 1, 0.781 for Observer 2, and 0.817 after averaging the 2 observers. The results from this study provide a supine reference for sagittal spine alignment using the Cobb method for both CT scans and plain radiographs. It also demonstrates the high degree of reliability between measurements from 2 imaging sources and various observers as shown with the ICC values.

Web-links as a means to document annotated sequence and 3D-structure alignments in systems biology.

Reconstructed biological networks are the essence of knowledge originating from experiments, scientific literature, databases and modeling. Proteins are the major players in biological networks. If the function of a protein is not yet known, it can often be deduced from homologous proteins that are already experimentally characterized. As such conclusions are not as reliable as experimental evidences, they should be well documented and reviewed when experimental data is available. Inconsistent operation of the resulting network may indicate invalid functional assignments. Here we present a novel technique to refer to annotated sequence and 3D-structure alignments in terms of Web links. By clicking the Web link the alignment is viewed in the protein viewer STRAP. References to public protein databases such as EMBL, KEGG, GENBANK, PDB, PFAM, PRODOM and UNIPROT/SWISSPROT are encoded in the Web-link whereas the alignment gaps are computed dynamically. Site specific annotations and 3D-rendering commands may also be included in the Web-link. In contrast, sequence features such as active site residues, phosphorylation sites and ligand binding sites do not need to be specified, as long as they are retrievable from public databases. The method has been developed for an information management system that is used for the reconstruction of metabolic pathways. The alignment viewer may also be of interest for experimentalists, as it can be used to document sites of interest in the proteins under experimental investigation. These alignment Web links may be included in project Web sites. The STRAP program is published under the GNU-license condition and is automatically downloaded from http://3d-alignment.eu/ or http://www.charite.de/bioinf/strap/ when an alignment reference is clicked.

Towards valid and reusable reference alignments — ten basic quality checks for ontology alignments and their application to three different reference data sets

Identifying relationships between hitherto unrelated entities in different ontologies is the key task of ontology alignment. An alignment is either manually created by domain experts or automatically by an alignment system. In recent years, several alignment systems have been made available, each using its own set of methods for relation detection. To evaluate and compare these systems, typically a manually created alignment is used, the so-called reference alignment. Based on our experience with several of these reference alignments we derived requirements and translated them into simple quality checks to ensure the alignments’ validity and also their reusability. In this article, these quality checks are applied to a standard reference alignment in the biomedical domain, the Ontology Alignment Evaluation Initiative Anatomy track reference alignment, and two more recent data sets covering multiple domains, including but not restricted to anatomy and biology.

Instance-based Semantic Interoperability in the Cultural Heritage

This paper gives a comprehensive overview over the problem of Semantic Interoperability in the Cultural Heritage domain, with a particular tbcus on solutions centered around extensional, i.e., instance-based, ontology matching methods. It presents three typical scenarios requiring interoperability, one with homogeneous collections, one with heterogeneous collections, and one with multi-lingual collections. It discusses two different ways to evaluate potential alignments, one based on the application of re-indexing, one using a reference alignment. To these scenarios we apply extensional matching with different similarity measures, which gives interesting insight into the applicability of this matching approach. Finally, we firmly position our work in the Cultural Heritage context through an extensive discussion of the relevance for, and isstles related to this specific field. The findings are as unspectacular as expected, but nevertheless important: the provided methods can really improve interoperability in a number of important cases, but they are not universal solutions to all related problems. This paper provides a solid foundation for any future work on Semantic Interoperability in the Cultural Heritage domain, in particular tbr anybody intending to apply extensional methods.

Genome-Wide Genotyping of Acute Myeloid Leukemia with t(9;11) Reveals New Recurrent Genomic Alterations,

Abstract 3546Rearrangements of the mixed lineage leukemia (MLL) gene are associated with the development of acute leukemia, and a variety of translocation partners have been described to date. In acute myeloid leukemia (AML), the translocation t(9;11)(p22;q23), resulting in the MLLT3-MLL fusion gene, is the most common genetic event involving MLL. The translocation t(9;11) can occur de novo, or as a consequence of previous chemotherapy (t-AML). Both types exhibit significant biological and clinical heterogeneity, and cooperating genetic events have been implicated underlying these heterogeneous phenotypes. To identify additional genomic abnormalities in AML with t(9;11), we performed high-resolution, genome-wide analysis of DNA copy number alterations (CNA) and copy neutral loss of heterozygosity (CN-LOH) using Affymetrix 6.0 single nucleotide polymorphism (SNP) microarrays in 34 AMLs with t(9;11) [de novo AML, n=22; t-AML, n=12]. Samples were also analyzed for AML-associated mutations: FLT3 [internal tandem duplication (ITD; 2/33); tyrosine kinase domain (TKD; 2/26)], NPM1 (0/28), CEBPA (0/23), IDH1 (0/28), IDH 2 (0/28), DNMT3A (0/19), NRAS (0/6); and deregulated expression of EVI1 (8/16). Control DNA from remission bone marrow or peripheral blood was available for paired analysis in 12 (33%) cases. Data were processed using reference alignment, dChipSNP, and circular binary segmentation. Paired analysis revealed a mean of 1.9 somatic CNAs per case (range: 0–12); 45% of cases lacked any CNAs. Deletions were more common than gains (1.73 losses/case vs. 0.25 gains/case; p =0.04). There were no significant differences in the mean number of CNAs between de novo and therapy-related cases (de novo AML: 1.0, range: 0–2; t-AML: 2.7, range: 0–12; p =0.93). Recurrent deletions were detected at chromosomal bands 7q36.1–36.2 (n=2) and at the chromosomal translocation breakpoint at 11q23 (n=2). The del(7q36.1–36.2) overlapped with a minimally deleted region at 7q36.1 that we previously identified in 8% of core-binding factor AML containing only 4 genes (PRKAG2, GALNT11, GALNTL5 and MLL3). The only gene contained in both regions was MLL3, a member of the mixed-lineage leukemia gene family. The most recurrent CNA was trisomy 8 (n=5), also detected by conventional cytogenetics in all 5 cases. Novel recurrent focal gains were identified at 9p22.1 (n=2; size: 341 Kb) and at 13q21.33-q22.1 (n=2; size: 1021 Kb) with each region containing genes potentially involved in cancer pathogenesis (ACER2 in 9p; KLF5 in 13q). Analysis of CN-LOH revealed no such lesion in any of the cases. In summary, our data provide a comprehensive survey of CNAs in a well characterized cohort of AMLs with t(9;11). These data demonstrate a very low occurrence of CNAs, with no significant differences between de novo and therapy-related cases and complete absence of CN-LOH. Interestingly, a number of novel recurrent secondary genetic alterations were identified. Determining the functional role of these lesions in leukemogenesis and drug resistance should provide new insights into t(9;11)-bearing AMLs. Disclosures:No relevant conflicts of interest to declare.

Protein sequence alignment with family-specific amino acid similarity matrices

BackgroundAlignment of amino acid sequences by means of dynamic programming is a cornerstone sequence comparison method. The quality of alignments produced by dynamic programming critically depends on the choice of the alignment scoring function. Therefore, for a specific alignment problem one needs a way of selecting the best performing scoring function. This work is focused on the issue of finding optimized protein family- and fold-specific scoring functions for global similarity matrix-based sequence alignment.FindingsI utilize a comprehensive set of reference alignments obtained from structural superposition of homologous and analogous proteins to design a quantitative statistical framework for evaluating the performance of alignment scoring functions in global pairwise sequence alignment. This framework is applied to study how existing general-purpose amino acid similarity matrices perform on individual protein families and structural folds, and to compare them to family-specific and fold-specific matrices derived in this work. I describe an adaptive alignment procedure that automatically selects an appropriate similarity matrix and optimized gap penalties based on the properties of the sequences being aligned.ConclusionsThe results of this work indicate that using family-specific similarity matrices significantly improves the quality of the alignment of homologous sequences over the traditional sequence alignment based on a single general-purpose similarity matrix. However, using fold-specific similarity matrices can only marginally improve sequence alignment of proteins that share the same structural fold but do not share a common evolutionary origin. The family-specific matrices derived in this work and the optimized gap penalties are available at http://taurus.crc.albany.edu/fsm.

Comparison of linear gap penalties and profile-based variable gap penalties in profile–profile alignments

Profile–profile alignment algorithms have proven powerful for recognizing remote homologs and generating alignments by effectively integrating sequence evolutionary information into scoring functions. In comparison to scoring function, the development of gap penalty functions has rarely been addressed in profile–profile alignment algorithms. Although indel frequency profiles have been used to construct profile-based variable gap penalties in some profile–profile alignment algorithms, there is still no fair comparison between variable gap penalties and traditional linear gap penalties to quantify the improvement of alignment accuracy. We compared two linear gap penalty functions, the traditional affine gap penalty (AGP) and the bilinear gap penalty (BGP), with two profile-based variable gap penalty functions, the Profile-based Gap Penalty used in SP5 (SPGP) and a new Weighted Profile-based Gap Penalty (WPGP) developed by us, on some well-established benchmark datasets. Our results show that profile-based variable gap penalties get limited improvements than linear gap penalties, whether incorporated with secondary structure information or not. Secondary structure information appears less powerful to be incorporated into gap penalties than into scoring functions. Analysis of gap length distributions indicates that gap penalties could stably maintain corresponding distributions of gap lengths in their alignments, but the distribution difference from reference alignments does not reflect the performance of gap penalties. There is useful information in indel frequency profiles, but it is still not good enough for improving alignment accuracy when used in profile-based variable gap penalties. All of the methods tested in this work are freely accessible at http://protein.cau.edu.cn/gppat/.