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PubMed2004

Transport of tools to food sites in tufted capuchin monkeys (Cebus apella).

Tool use and transport represent cognitively important aspects of early hominid evolution, and nonhuman primates are often used as models to examine the cognitive, ecological, morphological and social correlates of these behaviors in order to gain insights into the behavior of our early human ancestors. In 2001, Jalles-Filho et al. found that free-ranging capuchin monkeys failed to transport tools (stones) to food sites (nuts), but transported the foods to the tool sites. This result cast doubt on the usefulness of Cebus to model early human tool-using behavior. In this study, we examined the performance of six captive tufted capuchin monkeys (Cebus apella) in a tool transport task. Subjects were provided with the opportunity to transport two different tools to fixed food reward sites when the food reward was visible from the tool site and when the food reward was not visible from the tool site. We found that the subjects quickly and readily transported probing tools to an apparatus baited with syrup, but rarely transported stones to a nut-cracking apparatus. We suggest that the performance of the capuchins here reflects an efficient foraging strategy, in terms of energy return, among wild Cebus monkeys.

Animals↗

PubMed1993

Pneumatic tool torque reaction: reaction forces, displacement, muscle activity and discomfort in the hand-arm system.

Reaction forces, hand-arm displacement, muscle activity and discomfort ratings were studied during the securing of threaded fasteners with three angle nutrunners with different shut-off mechanisms, but with the same spindle torque (72-74 Nm). The three tools were tested according to the method specified in ISO 6544. One of the tools had an almost instantaneous shut-off. Another had a more slowly declining torque curve. For the third tool the maximum torque was maintained for a while before shut-off. Twelve male subjects participated in the study. A force platform measured the reaction force between the subject and the floor. The option of the hand-arm system and the shoulder was measured with an optoelectronic measuring system. The muscle activity (EMG) in six muscles in the arm and shoulder was measured with surface electrodes. Significant differences in the arm movements and ground reaction forces were found between the three tools. The smallest values were found with the fast shut-off tool while the delayed shut-off tool caused the largest values. The EMG measures gave inconsistent response patterns. Discomfort ratings were highly correlated with the time for which the tool torque exceeded 90% of peak preset torque, but the time for which the tool torque exceeded 90% of peak calculated by the method specified in ISO 6544. Nutrunners with a shut-off mechanism that causes a slowly decreasing torque or a torque that is maintained for a while before shut-off should be avoided. If no substitutes are available, then a torque reaction bar should be mounted on the tool.

Journal Article↗

PubMed1994

Integrated software tools for the evaluation of radiotherapy treatment plans.

PURPOSE: This article announces the availability of a convenient and useful software environment for the evaluation of three-dimensional (3D) radiotherapy treatment plans. MATERIALS AND METHODS: Using standards such as American National Standards for Information Systems C and the X Window System allowed us to bring the computation and display of dose-volume histograms, dose statistics, tumor control probabilities, normal tissue complication probabilities, and a figure of merit together under one user interface. These plan evaluation tools are not stand alone, but must interact with a 3D radiation therapy planning system to obtain the required dose matrices and patient anatomical contours. Installation of the software involves a programmer who writes a software bridge between the radiation therapy planning system and the tools, thereby providing access to local data files. This design strategy confines portability issues to one area of the software. RESULTS: Access to the other tools is through the Graphical Plan Evaluation Tool (GPET). GPET coordinates the use of each of the tools and provides graphical facilities for display of their results. Importantly, GPET assures that the displayed results of each tool have been computed with the same input specifications for all treatment plans being compared. For added convenience, the user can rearrange the resultant data to be reviewed in various ways on the video screen. The software design also allows incorporation of customized algorithms and input data for computing tumor control probability and normal tissue complication probabilities, since those currently available are controversial. CONCLUSION: The Graphical Plan Evaluation Tool unifies the simultaneous computation for several analytical tools and graphical display of their results. Within the constraints of the X Window System environment, this assemblage of software tools provides a portable, flexible, and convenient method for the quantitative evaluation of several radiotherapy treatment plans.

Dose-Response Relationship, Radiation↗

PubMed1995

The cumulative verification image analysis tool for offline evaluation of portal images.

PURPOSE: Daily portal images acquired using electronic portal imaging devices contain important information about the setup variation of the individual patient. The data can be used to evaluate the treatment and to derive correction for the individual patient. The large volume of images also require software tools for efficient analysis. This article describes the approach of cumulative verification image analysis (CVIA) specifically designed as an offline tool to extract quantitative information from daily portal images. METHODS AND MATERIALS: The user interface, image and graphics display, and algorithms of the CVIA tool have been implemented in ANSCI C using the X Window graphics standards. The tool consists of three major components: (a) definition of treatment geometry and anatomical information; (b) registration of portal images with a reference image to determine setup variation; and (c) quantitative analysis of all setup variation measurements. The CVIA tool is not automated. User interaction is required and preferred. Successful alignment of anatomies on portal images at present remains mostly dependent on clinical judgment. Predefined templates of block shapes and anatomies are used for image registration to enhance efficiency, taking advantage of the fact that much of the tool's operation is repeated in the analysis of daily portal images. RESULTS: The CVIA tool is portable and has been implemented on workstations with different operating systems. Analysis of 20 sequential daily portal images can be completed in less than 1 h. The temporal information is used to characterize setup variation in terms of its systematic, random and time-dependent components. The cumulative information is used to derive block overlap isofrequency distributions (BOIDs), which quantify the effective coverage of the prescribed treatment area throughout the course of treatment. Finally, a set of software utilities is available to facilitate feedback of the information for treatment plan recalculation and to test various decision strategies for treatment adjustment. CONCLUSIONS: The CVIA tool provides comprehensive analysis of daily images acquired with electronic portal imaging devices. Its offline approach allows characterization of the nature of setup variation for the individual patient that would have been difficult to deduce using only a few daily or weekly portal images. Distribution of the tool will help establish an important database of setup variation from many clinics. The information derived from CVIA can also serve as the foundation to integrate treatment verification, treatment planning, and treatment delivery.

Computer Peripherals↗

PubMed2006

Pain assessment tools: is the content appropriate for use in palliative care?

Inadequate pain assessment prevents optimal treatment in palliative care. The content of pain assessment tools might limit their usefulness for proper pain assessment, but data on the content validity of the tools are scarce. The objective of this study was to examine the content of the existing pain assessment tools, and to evaluate the appropriateness of different dimensions and items for pain assessment in palliative care. A systematic search was performed to find pain assessment tools for patients with advanced cancer who were receiving palliative care. An ad hoc search with broader search criteria supplemented the systematic search. The items of the identified tools were allocated to appropriate dimensions. This was reviewed by an international panel of experts, who also evaluated the relevance of the different dimensions for pain assessment in palliative care. The systematic literature search generated 16 assessment tools while the ad hoc search generated 64. Ten pain dimensions containing 1,011 pain items were identified by the experts. The experts ranked intensity, temporal pattern, treatment and exacerbating/relieving factors, location, and interference with health-related quality of life as the most important dimensions. None of the assessment tools covered these dimensions satisfactorily. Most items were related to interference (231) and intensity (138). Temporal pattern (which includes breakthrough pain), ranked as the second most important dimension, was covered by 29 items only. Many tools include dimensions and items of limited relevance for patients with advanced cancer. This might reduce compliance and threaten the validity of the assessment. New tools should reflect the clinical relevance of different dimensions and be user-friendly.

Humans↗

PubMed1998

Why some capuchin monkeys (Cebus apella) use probing tools (and others do not).

Tufted capuchins (Cebus apella) were provided with a task that facilitated the use and modification of sticks as probing tools. It was found that subjects aged 10 years or older at initial task exposure were less likely to use tools than were younger subjects. Furthermore, juveniles whose mothers died before the subjects were aged 3 years were less likely to use tools than were juveniles whose mothers survived through this period. The ability to use tools was not related to subject sex or to access to the tool site or raw tool materials. Subjects modified tools both before and during their use, and the relative percentage of tools modified increased with subject age. Thus, it appears that capuchins most readily acquire tool use before the age of 10 years and that early disruption of the mother-infant relationship has deleterious effects on the emergence of instrumental behavior.

Aging↗

PubMed2003

Translating clinical tools in nursing practice.

BACKGROUND: The widespread use of clinical tools in nursing practice reflects their usefulness in guiding patient care, evaluating treatment effectiveness and conducting audit. Cultural awareness and the provision of culturally competent care is a high priority for nurses in the United Kingdom (UK), given patterns of increasing ethnic diversity. However, meeting the individual needs of patients can be difficult when language barriers hinder communication. One way to address these difficulties is to translate existing clinical tools. AIM: The aim of this paper is to appraise the potential for, and limitations of, translating clinical tools for use in nursing practice. DISCUSSION: Drawing on a range of studies from the disciplines of health and social science, this review describes and discusses some key considerations relevant to translating clinical tools in nursing. These considerations include the need to ensure cultural equivalence, lack of familiarity with clinical tool formats in some cultures and its impact on responses, and low literacy levels in some populations. CONCLUSION: Clinical tools provide benefits in identifying patients' problems, guiding patient care, and evaluating treatments and interventions. Translating these tools can help to bridge the language gap that hinders good communication between nurses and patients. Translated clinical tools can be of acceptable cultural equivalence and validity if high quality translation methodologies are employed, together with an awareness of culturally relevant issues when interpreting the information gained from the tools.

Communication Barriers↗

PubMed2003

Introducing a nutrition screening tool: an exploratory study in a district general hospital.

BACKGROUND: Concerns have been raised that patients' nutrition is a neglected aspect of care. Accordingly, 'nutrition screening tools' have been devised to ensure that all patients are assessed by nurses and, where appropriate, referred to dieticians. The tool adopted in our hospital was the 'Nursing Nutritional Screening Tool'. AIM: To investigate the impact of this screening tool on: nutrition-related nursing documentation; patient care at mealtimes; dietician referral. METHODS: This study was conducted on two similar general medical wards in a United Kingdom (UK) district general hospital, with the help of staff and patients (n = 175) admitted during two study periods, May 1999 and January 2000. Data were collected over 28 days before and after introduction of the screening tool on one of the wards. For both wards, in each stage of the study, data were collected b: review of patients' notes, non-participant observations of mealtimes. Frequencies of dietician referral and documentation of weight were compared by cross-tabulations and chi2 tests. Nine months later, the findings were discussed with ward sisters in a group interview. FINDINGS: Introduction of the screening tool impacted on the process but not the outcomes of screening. Use of the screening tool increased the frequency of nutrition-related documentation: the proportion of patients with weights recorded increased on the intervention ward (P < 0.001), and decreased on the comparator ward. Frequency of dietician referral decreased on both wards, but differences were statistically insignificant. There was no observable change in patient care at mealtimes. The nurses in charge of the wards felt that introduction of the screening tool had raised awareness of nutrition-related care. CONCLUSIONS: Meeting patients' nutritional needs is a complex aspect of care which may benefit from introduction of structured guidelines. However, the potential of screening tools to improve care is limited by diverse factors, which warrant further exploration.

Adolescent↗

PubMedDate not supplied

Use of a pain assessment and intervention notation (P.A.I.N.) tool in critical care nursing practice: nurses' evaluations.

BACKGROUND: One of the barriers to effective pain management in critical care is the lack of systematic, comprehensive methods for assessing and treating pain. Use of a printed, standardized pain assessment and intervention tool can stimulate critical thinking and provide a framework for organizing pain assessment and management data. OBJECTIVES: The objectives of this study were to do the following: (1) describe the Pain Assessment and Intervention Notation (P.A.I.N.) tool, (2) detail critical care nurse participants' evaluations of the P.A.I.N. intervention tool when used during care of postoperative patients in pain, and (3) evaluate the tool's usefulness in practice and education. METHODS: Eleven intensive care unit (n = 7) and postanesthesia care unit (n = 4) nurses completed a questionnaire after they had used the pain tool in their clinical practices with 31 postoperative patients. RESULTS: Ten of the 11 nurses who returned an evaluation questionnaire found that the P.A.I.N. tool provided a consistent, systematic method of quantifying their assessment of patient pain and analgesic responsiveness. Five nurse participants believed that the P.A.I.N. tool improved their practice with regard to pain and sedation assessment. Three of the 11 nurses believed that the usefulness of the tool was limited because it was too detailed to be used routinely when caring for critically ill patients. All but 1 of the 11 nurses believed that the tool would have helped them earlier in their practice (ie, when they had less critical care nursing experience). CONCLUSIONS: The assessment and treatment of pain in critically ill patients are highly complex processes. This study identified many advantages of the use of a standardized, systematic approach to pain assessment and treatment by health professionals.

Adult↗

PubMed2005

Development of a novel nutrition screening tool for use in elderly South Africans.

OBJECTIVE: To develop a nutrition screening tool for use in older South Africans. DESIGN: A cross-sectional validation study in 283 free-living and institutionalised black South Africans (60+ years). METHODS: Trained field-workers administered a 24-hour recall and the Mini Nutritional Assessment (MNA) screening tool, and performed anthropometric measurements and physical function tests. Cognitive function was assessed using a validated version of the Six-Item Cognitive Impairment Test. Biochemical indicators assessed included serum albumin, haemoglobin, ferritin, vitamin B12, red-blood-cell folate, cholesterol and vitamin C. The MNA was used as the gold standard against which a novel screening tool was developed using a six-step systematic approach, namely: correspondence analysis; identification of key questions; determination of internal consistency; correlational analyses with objective measures; determination of reference cut-off values for categories of nutritional risk; and determination of sensitivity and specificity. RESULTS: The new screening tool includes nine separate concepts, comprising a total of 14 questions, as well as measurement of mid-upper arm circumference. The new tool score was positively associated with level of independence in either basic activities of daily living (r = 0.472) or the more complex instrumental activities of daily living (r = 0.233). A three-category scoring system of nutritional risk was developed and shown to significantly characterise subjects according to physical function tests, level of independence and cognitive function. The new tool has good sensitivity (87.5%) and specificity (95.0%) compared with the MNA scoring system. It has a very high negative predictive value (99.5%), which means that the tool is unlikely to falsely classify subjects as well nourished/at risk when they are in fact malnourished. CONCLUSION: A novel screening tool has been shown to have content-, construct- and criterion-related validity, and the individual items have been shown to have good internal consistency. Further validation of the tool in a new population of elderly Africans is warranted.

Activities of Daily Living↗

PubMed2005

Ergonomics applications of a mechanical model of the human operator in power hand tool operation.

Applications of a new model for predicting power threaded-fastener-driving tool operator response and capacity to react against impulsive torque reaction forces are explored for use in tool selection and ergonomic workplace design. The model is based on a mechanical analog of the human operator, with parameters dependent on work location (horizontal and vertical distances); work orientation (horizontal and vertical); and tool shape (in-line, pistol grip, and right angle); and is stratified by gender. This model enables prediction of group means and variances of handle displacement and force for a given tool configuration. Response percentiles can be ascertained for specific tool operations. For example, a sample pistol grip nutrunner used on a horizontal surface at 30 cm in front of the ankles and 140 cm above the floor results in a predicted mean handle reaction displacement of 39.0 (SD=28.1) mm for males. Consequently 63%of the male users exceed a 30 mm handle displacement limit. When a right angle tool of similar torque output is used instead, the model predicted that only 4.6%of the male tool users exceed a 30 mm handle displacement. A method is described for interpolating individual subject model parameters at any given work location using linear combinations in relation to the range of modeled factors. Additional examples pertinent to ergonomic workstation design and tool selection are provided to demonstrate how the model can be used to aid tool selection and workstation design.

Adult↗

PubMed1998

Understanding articles describing clinical prediction tools. Evidence Based Medicine in Critical Care Group.

OBJECTIVES: Clinical prediction rules and models are developed by applying statistical techniques to find combinations of predictors that categorize a heterogeneous group of patients into subgroups of risk. Our goal is to teach clinicians how to evaluate the validity, results, and applicability of articles describing clinical prediction tools. CLINICAL EXAMPLE: An article describing a rule to predict the need for intensive care unit care admission in patients presenting to the emergency room with chest pain. RECOMMENDATIONS: Valid clinical prediction tools are developed by completely following up a representative group of patients, by evaluating all potential predictors and testing the independent contribution of each predictor variable, and by ensuring that the outcomes were independent of the predictors. To evaluate the results of an article describing a clinical prediction tool, clinicians need to know what the prediction tool is, how well it categorizes patients into different levels of risk, and what the confidence intervals are around the risk estimates. Valid prediction tools are not applicable in every patient population. Before patient care application, the clinician should ensure that the tool maintains its prediction power in a new sample of patients, that the patients are similar to patients used to test the tool, and that the tool has been shown to improve clinical decision-making. CONCLUSIONS: There has been an increase in the development and validation of clinical prediction rules and models. It is important to evaluate the validity and reliability of these prediction tools before application.

APACHE↗

PubMed2000

Human-like, population-level specialization in the manufacture of pandanus tools by New Caledonian crows Corvus moneduloides.

The main way of gaining insight into the behaviour and neurological faculties of our early ancestors is to study artefactual evidence for the making and use of tools, but this places severe constraints on what knowledge can be obtained. New Caledonian crows, however, offer a potential analogous model system for learning about these difficult-to-establish aspects of prehistoric humans. I found new evidence of human-like specialization in crows' manufacture of hook tools from pandanus leaves: functional lateralization or 'handedness' and the shaping of these tools to a rule system. These population-level features are unprecedented in the tool behaviour of free-living non-humans and provide the first demonstration that a population bias for handedness in tool-making and the shaping of tools to rule systems are not concomitant with symbolic thought and language. It is unknown how crows obtain their tool behaviour. Nevertheless, at the least they can be studied in order to learn about the neuropsychology associated with early specialized and/or advanced population features in tool-making such as hook use, handedness and the shaping of tools to rule systems.

Animals↗

PubMed2000

Assessment of pain in cognitively impaired older adults: a comparison of pain assessment tools and their use by nonprofessional caregivers.

OBJECTIVES: To compare self-reporting of pain by cognitively impaired (CI) older adults living in the community with reports of their caregivers; to identify the factors associated with differences in agreement; and to identify those pain assessment tools that are most useful to nonprofessional caregivers. DESIGN: Prospective observational cohort of patients with dementia and their caregivers. SETTING: In-home assessments of community-dwelling CI older adults and family members, adult foster care providers, or aides in residential care facilities. All CI subjects were enrolled in a Program for All-inclusive Care of the Elderly program (ElderPlace) in Portland, Oregon. PARTICIPANTS: A total of 156 CI adults and their caregivers. METHODS: Standardized pain assessment instruments were administered to the CI subjects and their caregivers in the subject's home by trained research assistants between June and October 1998. CI subjects were assessed with the Nonverbal Visual Analog scale ("line"), the Faces Pain Scale ("faces"), and the Philadelphia Pain Intensity Scale (PIS). Research assistants observed pain behaviors in the CI subjects using the Hospice Approach Discomfort Scale. The CI subject's caregivers completed the "line," "faces," PIS, and Cornell Scale for Depression in Dementia. A baseline Mini-Mental State Exam, Functional Assessment Stage Test, and Geriatric Depression Scale were performed on all CI subjects by ElderPlace medical, nursing, or social work staff. RESULTS: The mean age of the CI subjects was 83, and 83% were women. The mean Mini-Mental State Exam score was 15.7. One-third of the CI subjects were unable to complete any of the three pain assessment tools. Of the 104 subjects completing at least one tool, 13 (12.5%) reported no pain and 91 (87.5%) reported some pain. Sixteen (10%) of the subjects were depressed as measured with the GDS or Cornell instrument. In 70 of the 104 subjects (67%) able to complete any tool, the caregiver and CI subject agreed as to the level of pain experienced by the CI subject. The number of tools completed by the CI subjects decreased with increased cognitive impairment. The Pain Intensity Scale was the tool most likely to be completed by both CI subjects and caregivers. The means of test scores were not significantly different for the paired groups of CI subject and caregiver, and the nonparametric correlation of each tool was significant: "faces" (Spearman's rho (p) = .417); "line" (p = .420); and PIS (p = .452). The Hospice Approach Discomfort Scale did not correlate well with other tools. The Pain Intensity Scale seems to be more useful than other pain assessment tools in assessing pain in cognitively impaired patients and can be used by nonprofessional caregivers in a community-based care setting.

Aged↗

PubMed2006

Development and testing of tools to assess physical restraint use.

BACKGROUND: To implement best practice in restraint use, healthcare providers and decision makers require current, accurate, and easily accessible information about restraint practices in their setting. There is a need for a reliable and valid instrument that is feasible for use in these settings to rapidly assess physical restraint use. METHOD: Two instruments to assess physical restraint use were developed and tested: an observation tool and a chart audit. The instruments were tested in complex continuing care units and rehabilitation units at two healthcare organizations. The restraint use observation tool was administered by trained observers in a series of five observations over a 2-week period. Chart audits were conducted for a sample of residents. Inter-rater agreement of the observation tool and chart audit was assessed. Point prevalence estimates were obtained for each site. The time required to use the observation tool and complete chart audits as well as the comparability of findings from the two data sources were described. FINDINGS: Restraint use observations were completed for 289 patients and chart audits were completed for 207 patients. Prevalence and patterns of restraint use varied between sites and across time periods. Observations took an average of 2.6 (Site A) and 0.6 (Site B) minutes per patient. There was excellent inter-rater agreement for most items on the observation tool with the exception of whether or not the patient was able to release or loosen the restraint. There was significant concordance but as expected, not complete agreement between paired estimates of prevalence using the observational tool and the chart audit. CONCLUSION: The observation and chart audit tools are feasible to use and reliably assess physical restraint use in healthcare organizations. The patient's physical capacity to move independently, the patient's waking status, and the restraint's restriction of mobility are items that should be added to the observation tool. The tools are complementary and should be used in tandem to capture the multifaceted complexity of restraint use in health service organizations.

Adolescent↗

PubMedDate not supplied

Oral tool use by captive orangutans (Pongo pygmaeus).

Eight captive orangutans (Pongo pygmaeus) were given wooden blocks embedded with raisins and bamboo as raw material for tool making in a study of manual laterality. In about three quarters of the raisin extraction bouts, the orangutans held the tool in the lips or teeth rather than in their hands. Three adult males and 2 adult females showed extreme (> or =92%) preference for oral tool use, a subadult male and an adult female used oral tools about half the time, and 1 adult female preferred manual tool use. Most oral tool users made short tools (approx. 4-10 cm long) that were held in the lips and (probably) supported by the tongue. Preference for oral tool use does not correlate with body weight, age or sex, but it may be related to hand size or individual preference. This is the first report of customary oral tool use as the norm in captive orangutans; it resembles the behavioral patterns reported by van Schaik et al. and Fox et al. in nature.

Animals↗

PubMed2002

Evaluation of a rapid field tool for assessing household diet quality in Mozambique.

The Nutrition Section of the Mozambican Ministry of Health recently implemented a low-cost, rapid field tool for assessing the quality of household diets. Such tools can play an important part in targeting development assistance in countries where resources are scarce. This paper evaluates how well the tool performs at describing household dietary intakes in northern Mozambique and explores ways to improve it. The food-group classification and scoring system that form the core of the tool were applied to household data (n = 1,140) collected in a previous quantitative diet study in Nampula and Cabo Delgado Provinces. Using mean intakes as a criterion, the diet assessment tool performed well on all nutrients studied, except vitamin A. Those classified by the tool into the top group of diet quality had the highest mean intakes of energy, protein, and iron as well as the highest mean scores on the Mozambican Diet Quality Index, whereas those classified in the bottom group had the lowest intakes. Sensitivity rates for the diet assessment tool could be substantially improved by raising the cutoff point for an acceptable diet from the current threshold of 20 points to 23 points. Regression analysis was used to suggest other possible improvements. Such improvements were only marginal and do not justify field implementation, given the added complexity in classifying and scoring. This paper provides evidence that, with some minor changes, the Ministry of Health diet assessment method can be a useful tool in describing the dietary situation of groups of Mozambican households. Since this tool is both inexpensive and simple to use, there may be interest in adapting it for use in other low-income countries. A series of steps for doing so is outlined at the end of this paper.

Diet↗

PubMed2004

Benchmarking tools for the alignment of functional noncoding DNA.

BACKGROUND: Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of protein-coding sequences typically have been benchmarked against "correct" alignments inferred from structural data. For noncoding sequences, where such independent validation is lacking, simulation provides an effective means to generate "correct" alignments with which to benchmark alignment tools. RESULTS: Using rates of noncoding sequence evolution estimated from the genus Drosophila, we simulated alignments over a range of divergence times under varying models incorporating point substitution, insertion/deletion events, and short blocks of constrained sequences such as those found in cis-regulatory regions. We then compared "correct" alignments generated by a modified version of the ROSE simulation platform to alignments of the simulated derived sequences produced by eight pairwise alignment tools (Avid, BlastZ, Chaos, ClustalW, DiAlign, Lagan, Needle, and WABA) to determine the off-the-shelf performance of each tool. As expected, the ability to align noncoding sequences accurately decreases with increasing divergence for all tools, and declines faster in the presence of insertion/deletion evolution. Global alignment tools (Avid, ClustalW, Lagan, and Needle) typically have higher sensitivity over entire noncoding sequences as well as in constrained sequences. Local tools (BlastZ, Chaos, and WABA) have lower overall sensitivity as a consequence of incomplete coverage, but have high specificity to detect constrained sequences as well as high sensitivity within the subset of sequences they align. Tools such as DiAlign, which generate both local and global outputs, produce alignments of constrained sequences with both high sensitivity and specificity for divergence distances in the range of 1.25-3.0 substitutions per site. CONCLUSION: For species with genomic properties similar to Drosophila, we conclude that a single pair of optimally diverged species analyzed with a high performance alignment tool can yield accurate and specific alignments of functionally constrained noncoding sequences. Further algorithm development, optimization of alignment parameters, and benchmarking studies will be necessary to extract the maximal biological information from alignments of functional noncoding DNA.

Animals↗