Sequence Entries Research Articles

Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A

BackgroundThe Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the α/β hydrolase fold. A new superfamily for Candida antarctica lipase A (CALA) was introduced including the recently published crystal structure of CALA. Since CALA has a highly divergent sequence in comparison to other α/β hydrolases, the Lipase Engineering Database was used to classify CALA in the frame of the already established classification system. This involved the comparison of CALA to similar structures as well as sequence-based comparisons against the content of the LED.ResultsThe new release 3.0 (December 2009) of the Lipase Engineering Database contains 24783 sequence entries for 18585 proteins as well as 656 experimentally determined protein structures, including the structure of CALA. In comparison to the previous release [1] with 4322 protein and 167 structure entries this update represents a significant increase in data volume. By comparing CALA to representative structures from all superfamilies, a structure from the deacetylase superfamily was found to be most similar to the structure of CALA. While the α/β hydrolase fold is conserved in both proteins, the major difference is found in the cap region. Sequence alignments between both proteins show a sequence similarity of only 15%. A multisequence alignment of both protein families was used to create hidden Markov models for the cap region of CALA and showed that the cap region of CALA is unique among all other proteins of the α/β hydrolase fold. By specifically comparing the substrate binding pocket of CALA to other binding pockets of α/β hydrolases, the binding pocket of Candida rugosa lipase was identified as being highly similar. This similarity also applied to the lid of Candida rugosa lipase in comparison to the potential lid of CALA.ConclusionThe LED serves as a valuable tool for the systematic analysis of single proteins or protein families. The updated release 3.0 was used for the evaluation of α/β hydrolases. The HTML version of the database with new features is available at http://www.led.uni-stuttgart.de and provides sequences, structures and a set of analysis tools including phylogenetic trees and HMM profiles

The Thiamine diphosphate dependent Enzyme Engineering Database: a tool for the systematic analysis of sequence and structure relations.

BackgroundThiamine diphosphate (ThDP)-dependent enzymes form a vast and diverse class of proteins, catalyzing a wide variety of enzymatic reactions including the formation or cleavage of carbon-sulfur, carbon-oxygen, carbon-nitrogen, and especially carbon-carbon bonds. Although very diverse in sequence and domain organisation, they share two common protein domains, the pyrophosphate (PP) and the pyrimidine (PYR) domain. For the comprehensive and systematic comparison of protein sequences and structures the Thiamine diphosphate (ThDP)-dependent Enzyme Engineering Database (TEED) was established.DescriptionThe TEED http://www.teed.uni-stuttgart.de contains 12048 sequence entries which were assigned to 9443 different proteins and 379 structure entries. Proteins were assigned to 8 different superfamilies and 63 homologous protein families. For each family, the TEED offers multisequence alignments, phylogenetic trees, and family-specific HMM profiles. The conserved pyrophosphate (PP) and pyrimidine (PYR) domains have been annotated, which allows the analysis of sequence similarities for a broad variety of proteins. Human ThDP-dependent enzymes are known to be involved in many diseases. 20 different proteins and over 40 single nucleotide polymorphisms (SNPs) of human ThDP-dependent enzymes were identified in the TEED.ConclusionsThe online accessible version of the TEED has been designed to serve as a navigation and analysis tool for the large and diverse family of ThDP-dependent enzymes.

Puumala virus reference strain for hantavirus serodiagnosis in France

Dear Editor, We read with great interest the paper of C. Strady et al. on leptospirosis and nephropathia epidemica (NE) in NorthEastern-France [1]. Herein, and as questioned already before [2], the authors refer once more to the French Institut Pasteur Humain or IPH strain 90-13 for screening Puumala virus (PUUV)-induced NE cases in France with IFA and/or ELISA. Isolation of this strain, announced as the first human PUUV isolate in France and in West-Europe, was published in 1995, and complete sequencing of its medium (M) RNA segment, respectively small (S) RNA segment was introduced in GenBank under respective accession numbers U22418 and U 22423 [3]. From the moment of its reported isolation in 1990, IPH 90-13 was acknowledged being more sensitive than other, nonautochthonous PUUV strains for picking up local French NE cases in IFA format [4]. However, a remarkable similarity was noted with CH 13891, a Belgian rodent strain already in use [4]. CH 13891 had been sent in 1987 by one of us (G vd G) to Pasteur Institute, Paris, in the frame of a Franco-Belgian collaboration to study emerging NE, and had been used successfully since then for serodiagnosing French NE cases, likewise in an IFA format [5]. This strain had been isolated in 1985 from a bank vole captured in the early ‘80s around Turnhout, North-Belgium [6], thus constituting in fact the earliest West-European PUUV isolate, available one year after Sotkamo, the prototype PUUV strain from Finland, and Hallnas from Sweden, both isolated in 1984. Moreover, the very first (1983) Belgian NE cases had been already serodiagnosed in IFA with this antigen, then called “Turnhout HFRS antigen” [7]. However, and as with so many other early hantavirus isolates (including also the Finnish Sotkamo) from the ‘80s pioneer times, CG 13891 was introduced in GenBank only years after a first characterisation, in this case finally in 1999. The Belgian rodent strain, isolated 5 years prior to the putative French human strain, appeared to have a 100% identical S and M RNA sequence pattern. The French and American authors of the original IPH 90-13 report concluded duly that a contamination with the Belgian CG 13891 had occurred earlier in the Paris lab, and published two successive Errata [8, 9]. They also corrected the GenBank situation, re-stating under accession numbers U22418 and U 22423 that “Sequence entry was originally reported as strain 90-13, but later found to be a laboratory contamination of strain CG 13891”. Nevertheless, many French clinicians and even serological labs continue nowadays to use the IPH 90-13 denomination for their serological diagnosis, thus referring in fact to a strain that is proven since 1999 to be non-existent [2]. In summary, and as confirmed again in the current study [1], the Paris and subsequently the Lyon reference labs for hemorrhagic fevers have been using from 1987 on CG 13891 in an IFA format, before adding from 2000 on an ELISA format, and later even a recombinant ELISA form, all derived from the same Belgian strain. In a technical paper describing the J. Clement (*) : P. Maes :M. Van Ranst Hantavirus Reference Centre, Laboratory of Clinical Virology & Rega Institute for Medical Research, University of Leuven, U.Z. Gasthuisberg, Herestraat, 49, B-3000 Leuven, Belgium e-mail: jan.clement@uzleuven.be

Megx.net: integrated database resource for marine ecological genomics.

Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. Access to data is facilitated by Web Services. The updated megx.net portal offers microbial ecologists greatly enhanced database content, and new features and tools for data analysis, all of which are freely accessible from our webpage http://www.megx.net.

The Lactamase Engineering Database: a critical survey of TEM sequences in public databases

BackgroundTEM β-lactamases are the main cause for resistance against β-lactam antibiotics. Sequence information about TEM β-lactamases is mainly found in the NCBI peptide database and TEM mutation table at . While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM β-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship.DescriptionThe LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM β-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM β-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM β-lactamase were common to both data sets. The 180 TEM β-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at and contains multisequence alignments, structure information and reconciled annotation of TEM β-lactamases. The LacED is weekly updated and supplies all data for download.ConclusionThe Lactamase Engineering Database enables a systematic analysis of TEM β-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM β-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur.

Electron‐capture dissociation (ECD), collision‐induced dissociation (CID) and ECD/CID in a linear radio‐frequency‐free magnetic cell

Electron‐capture dissociation (ECD), collision‐induced dissociation (CID) and ECD/CID in a linear radio‐frequency‐free magnetic cell

The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases

BackgroundPolyhydroxyalkanoates (PHAs) can be degraded by many microorganisms using intra- or extracellular PHA depolymerases. PHA depolymerases are very diverse in sequence and substrate specificity, but share a common α/β-hydrolase fold and a catalytic triad, which is also found in other α/β-hydrolases.ResultsThe PHA Depolymerase Engineering Database (DED, ) has been established as a tool for systematic analysis of this enzyme family. The DED contains sequence entries of 587 PHA depolymerases, which were assigned to 8 superfamilies and 38 homologous families based on their sequence similarity. For each family, multiple sequence alignments and profile hidden Markov models are provided, and functionally relevant residues are annotated.ConclusionThe DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes in silico, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.

UniquePrimer — a web utility for design of specific PCR primers and probes

We have developed a web-based tool for design of specific PCR primers and probes. The program allows you to enter primer sequence information as well as an optional probe, and sequence similarity searches (MegaBLAST) will be performed to see if the sequences match the same sequence entry in the specified database. If primers (and probe) match, this will be reported. The program can handle overlapping amplicons, amplification from a single primer, ambiguous bases and other problematic cases.

672: The paradoxical adrenergic signature of quiet sleep compatible with fetal heart-rate sequences

The association between antepartum fetal heart-rate short-term variability (STV) and fetal homeostatic evolutionary status is widely recognized. If taken into account that fetal stress resulting from homeostatic deviation is one possible source of the fetal cortisol crescendo suspected to induce labor, there might be a coincidence between antepartum STV decrease and a high fetal cortisol level. This coincidence could be accentuated if fetal cortisol induced – via identified receptors - fetal hippocampic neurosecretion, especially serotonin (the {{ sleep hormon }}), and acetylcholin (parasympathetic), thus possibly increasing quiet sleep (QS) parentheses occuring during active sleep (AS) behavioral sequences. If so, the third main hippocampic neurosecretion, noradrenalin, could induce paradoxical adrenergic signature during QS sequences. This signature has been observed after the birth by Heinz Zotter. Our objective was to evidence the suspected signature in antepartum. 100 unselected consecutive pregnancies had 110 minutes fetal heart-rate (FHR) on the average after 32 weeks. Graphical analysis identified typical QS via sudden entry and exit of a low STV sequence lasting several minutes. The adrenergic signature was judged to be either active [heart frequency (HF) increase at QS entry], passive [no basal HF variation], or absent [HF decrease at entry]. Typical QS sequences were observed in 39 cases: Passive signature: 26 cases, Active: 10 cases [7 evoking hippocampic implication and 3 adrenal implication. No signature: 3 cases. Antepartum fetal heart-rate could give indications about the fetal cortisol level. This notion could help to understand fetal pre-adaptation to labor, and parturition itself.

Quantitative Proteomics Reveals Regulation of Dynamic Components within TATA-binding Protein (TBP) Transcription Complexes

Affinity purification in combination with isotope labeling of proteins has proven to be a powerful method to discriminate specific from nonspecific interactors. However, in the standard SILAC (stable isotope labeling by amino acids in cell culture) approach dynamic components may easily be assigned as nonspecific. We compared two affinity purification protocols, which in combination revealed information on the dynamics of protein complexes. We focused on the central component in eukaryotic transcription, the human TATA-binding protein, which is involved in different complexes. All known TATA-binding protein-associated factors (TAFs) were detected as specific interactors. Interestingly one of them, BTAF1, exchanged significantly in cell extracts during the affinity purification. The other TAFs did not display this behavior. Cell cycle synchronization showed that BTAF1 exchange was regulated during mitosis. The combination of the two affinity purification protocols allows a quantitative approach to identify transient components in any protein complex.

Species identification of some common necrophagous flies in Guangdong province, southern China based on the rDNA internal transcribed spacer 2 (ITS2)

Recent studies suggest that sequence analysis technique displays a tempting foreground in identifying unknown specimens of necrophagous flies. In this study, we analyzed 63 complete ITS2 sequences concerning 29 fly species to evaluate the identification potential of the ITS2 region, among of which 41 sequence entries were obtained by sequencing and 22 sequence entries were available on the line. Additionally, phenetic method was recommended to substitute for phylogenetic method because it is very difficult to align the ITS2 sequences. The neighbor-joining tree generated by clustalx1.81 allowed us to differentiate each species. Meanwhile the tree topology also suggested that the ITS2 region showed no resolution for the distinction of geographical populations of some species. The overlapping between intra- and interspecific variation revealed by sequence analyses did not affect species identification. High sequence homology between some congeneric species required further sequencing for forensic practice.

Anti-lambda-light chain-peptide antibodies are suitable for the immunohistochemical classification of AL amyloid.

We aimed to test whether antibodies raised against recombinant peptides corresponding to the variable region of immunoglobulin light chains are suitable for the immunohistochemical classification of amyloid. The Entrez database of the National Center for Biotechnology Information (NCBI) was searched for all protein sequence entries which met the search criteria "amyloid" and "lambda light chain". Sixty-four different lambda-light chain-derived amyloid protein sequences were retrieved, aligned and categorized into the V region subgroups of lambda-light chain detailed by the NCBI, i.e. subgroup I (21 protein sequences), II (14), III (6), IV (1), V (1) and VI (21). V region subgroup I was chosen for epitope sequence selection and two rabbits were immunized with the following peptides: NH2-ISCSGSSSNIGSNTV-CONH2 and NH2-QRPSG VPDRFSGSKSGTS-CONH2. Sensitivity and specificity of the IgG-purified antibodies was tested by Western blotting using amyloid A- (AA), ALlambda- and ALkappa-amyloid proteins, and by immunohistochemistry on tissue microarrays with 110 different amyloid containing tissue samples obtained at autopsy from 22 patients, and on 27 biopsy specimens from a series of 24 patients. Our peptide antibodies specifically stained AL amyloid lambda-light chain-origin, in both Western blots and formalin-fixed and paraffin-embedded tissue sections, confirming that peptide-antibodies directed against immunoglobulin-derived lambda-light chain proteins can be applied for the immunohistochemical classification of amyloid. This offers the opportunity to generate a large set of anti-lambda-light chain protein-antibodies for the immunohistochemical classification of amyloid independently from native human tissue sources.

Identification of species of Abiotrophia, Enterococcus, Granulicatella and Streptococcus by sequence analysis of the ribosomal 16S–23S intergenic spacer region

The feasibility of sequence analysis of the ribosomal 16S-23S intergenic spacer region (ITS) was evaluated for identification of 24 species of Streptococcus, one species of Abiotrophia, 18 species of Enterococcus and three species of Granulicatella. As GenBank currently lacks ITS sequence entries for many species of these four genera, the ITS sequences of 38 type strains were first sequenced and submitted to GenBank to facilitate species identification of these genera. Subsequently, the ITS sequences of 217 strains (84 reference strains and 133 clinical isolates) were determined and species identification was made by blast search for homologous sequences in public databases. Species other than Streptococcus contained multiple ITS fragments and only the shortest fragment was analysed. A total of 25 isolates (11.5 %) produced discrepant identification by ITS sequencing. The 25 discordant strains were analysed further by sequencing of the 16S rRNA gene for species clarification, and 21 were found to be identified correctly by ITS sequence analysis. The correct identification rate by ITS sequencing was 98.2 % (213/217). Several closely related enterococcal and streptococcal species/subspecies contained specific ITS signature sequences that were useful for differentiating these bacteria. In conclusion, ITS sequencing provides a useful approach towards identifying this group of pathogens on a molecular platform alongside 16S rRNA gene sequencing.

Membrane Proteome Analysis of Microdissected Ovarian Tumor Tissues Using Capillary Isoelectric Focusing/Reversed-Phase Liquid Chromatography−Tandem MS

This work expands our tissue proteome capabilities from the analysis of soluble proteins in previous studies to the examination of membrane proteins within the pellets of enriched and selectively isolated tumor cells procured from microdissected tissue specimens. The pellets of targeted ovarian tumor cells are treated by two different membrane protein extraction methods, including the use of detergent and organic solvent. The detergent-based membrane protein preparation protocol not only extracts proteins effectively from cell pellets but also is compatible with subsequent proteome analysis using combined capillary isoelctric focusing/nano reversed-phase liquid chromatography separations coupled with nano electrospray ionization mass spectrometry. Among proteins identified from an amount of pellet equivalent to 20 000 cells, 773 proteins are predicted to contain one or more transmembrane domains, corresponding to 22% membrane proteome coverage within the SwissProt Human protein sequence entries.

ProFAT: a web-based tool for the functional annotation of protein sequences.

BackgroundThe functional annotation of proteins relies on published information concerning their close and remote homologues in sequence databases. Evidence for remote sequence similarity can be further strengthened by a similar biological background of the query sequence and identified database sequences. However, few tools exist so far, that provide a means to include functional information in sequence database searches.ResultsWe present ProFAT, a web-based tool for the functional annotation of protein sequences based on remote sequence similarity. ProFAT combines sensitive sequence database search methods and a fold recognition algorithm with a simple text-mining approach. ProFAT extracts identified hits based on their biological background by keyword-mining of annotations, features and most importantly, literature associated with a sequence entry. A user-provided keyword list enables the user to specifically search for weak, but biologically relevant homologues of an input query. The ProFAT server has been evaluated using the complete set of proteins from three different domain families, including their weak relatives and could correctly identify between 90% and 100% of all domain family members studied in this context. ProFAT has furthermore been applied to a variety of proteins from different cellular contexts and we provide evidence on how ProFAT can help in functional prediction of proteins based on remotely conserved proteins.ConclusionBy employing sensitive database search programs as well as exploiting the functional information associated with database sequences, ProFAT can detect remote, but biologically relevant relationships between proteins and will assist researchers in the prediction of protein function based on remote homologies.

16S rRNA Gene Sequencing and the Routine Clinical Microbiology Laboratory: a Perfect Marriage?

16S rRNA Gene Sequencing and the Routine Clinical Microbiology Laboratory: a Perfect Marriage?

Penaeus monodon gene discovery project: The generation of an EST collection and establishment of a database

A large-scale expressed sequence tag (EST) sequencing project was undertaken for the purpose of gene discovery in the black tiger shrimp Penaeus monodon. Initially, 15 cDNA libraries were constructed from different tissues (eyestalk, hepatopancrease, haematopoietic tissue, haemocyte, lymphoid organ, and ovary) of shrimp, reared under normal or stress conditions, to identify tissue-specific genes and genes responding to infection and heat stress. A total of 10,100 clones were analyzed by single-pass sequencing from the 5′ end. Clustering and assembling of these ESTs resulted in a total of 4845 unique sequences with 917 overlapping contigs and 3928 singletons. The redundancy of each cDNA library ranged from 13.4% to 61.3% with an overall redundancy of 61.1%. About half of these ESTs (2365 clones, 48.8%) showed significant homology (BLASTX, e-values < 10 − 4 ) to known genes. A high proportion of P. monodon ESTs was most similar to the predicted protein sequences from various organisms, e.g. Homo sapiens (9%), Mus musculus (7%) , Drosophila (6%), Gallus sp.(6%), and Anopheles (5%). Only 6% showed the highest similarity to other known genes from shrimp due to the limited sequence entries of the species in the public database. Several tissue-specific transcripts were identified as well as the candidate genes that may be implicated in the immune response. In addition, bioinformatic mining of microsatellites from the P. monodon ESTs identified 997 unique microsatellite containing ESTs in which 74 loci resided within the genes of known functions. Consequently, the P. monodon EST database was established. The EST sequence data and the BLAST results were stored and made available through a web-accessible database ( http://pmodon.biotec.or.th). This EST database provides a useful resource for gene identification and functional genomic studies of shrimp.

QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences

The quadruplex structures formed by guanine-rich nucleic acid sequences have received significant attention recently because of growing evidence for their role in important biological processes and as therapeutic targets. G-quadruplex DNA has been suggested to regulate DNA replication and may control cellular proliferation. Sequences capable of forming G-quadruplexes in the RNA have been shown to play significant roles in regulation of polyadenylation and splicing events in mammalian transcripts. Whether quadruplex structure directly plays a role in regulating RNA processing requires investigation. Computational approaches to study G-quadruplexes allow detailed analysis of mammalian genomes. There are no known easily accessible user-friendly tools that can compute G-quadruplexes in the nucleotide sequences. We have developed a web-based server, QGRS Mapper, that predicts quadruplex forming G-rich sequences (QGRS) in nucleotide sequences. It is a user-friendly application that provides many options for defining and studying G-quadruplexes. It performs analysis of the user provided genomic sequences, e.g. promoter and telomeric regions, as well as RNA sequences. It is also useful for predicting G-quadruplex structures in oligonucleotides. The program provides options to search and retrieve desired gene/nucleotide sequence entries from NCBI databases for mapping G-quadruplexes in the context of RNA processing sites. This feature is very useful for investigating the functional relevance of G-quadruplex structure, in particular its role in regulating the gene expression by alternative processing. In addition to providing data on composition and locations of QGRS relative to the processing sites in the pre-mRNA sequence, QGRS Mapper features interactive graphic representation of the data. The user can also use the graphics module to visualize QGRS distribution patterns among all the alternative RNA products of a gene simultaneously on a single screen. QGRS Mapper can be accessed at .

Current bioinformatics tools in genomic biomedical research (Review)

On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis. However, as sequence entries in the major genomic databases currently rise exponentially, the gap between available, deposited sequence data and analysis by means of conventional molecular biology is rapidly widening, making new approaches of high-throughput genomic analysis necessary. At present, the only effective way to keep abreast of the dramatic increase in sequence and related information is to apply biocomputational approaches. Thus, over recent years, the field of bioinformatics has rapidly developed into an essential aid for genomic data analysis and powerful bioinformatics tools have been developed, many of them publicly available through the World Wide Web. In this review, we summarize and describe the basic bioinformatics tools for genomic research such as: genomic databases, genome browsers, tools for sequence alignment, single nucleotide polymorphism (SNP) databases, tools for ab initio gene prediction, expression databases, and algorithms for promoter prediction.

Identification of Medically Important Yeast Species by Sequence Analysis of the Internal Transcribed Spacer Regions

Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as Pichia, Rhodotorula, Trichosporon, and Saccharomyces spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (Rhodotorula glutinis BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods.