Dataset Information

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

ABSTRACT:

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Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database.

Availability and implementation

MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2.

Contact

shallam@mail.ubc.ca

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Konwar KM

PROVIDER: S-EPMC4595896 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

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Publications

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

Konwar Kishori M KM Hanson Niels W NW Bhatia Maya P MP Kim Dongjae D Wu Shang-Ju SJ Hahn Aria S AS Morgan-Lang Connor C Cheung Hiu Kan HK Hallam Steven J SJ

Bioinformatics (Oxford, England) 20150615 20

<h4>Unlabelled</h4>Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation ...[more]

PMID: 26076725

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Project description:Study objectivesPoor sleep quality, a frequent problem in older adults, has been shown to be associated with reduced physical function and wellbeing. However, little is known about the relationship between sleep quality and the recovery of physical function following hospitalization. Thus, we conducted this study to examine the association between sleep quality and functional recovery after an acute hospitalization in community dwelling older adults.MethodsOlder adult patients (N = 23, mean age = 74 ± 9 years) were recruited during an acute hospitalization (average length of stay 3.9 days) with a cardiovascular (56%), pulmonary (22%), or metabolic (13%) admission diagnosis. Objective physical function was measured using the Short Physical Performance Battery (SPPB) and self-reported function was assessed with Katz Index of Independence in Activities of Daily Living (ADL) and Lawton Instrumental Activities of Daily Living Scale (IADL). Sleep quality was measured using Pittsburgh Sleep Quality Index (PSQI) global score and Iowa Fatigue Score (IFS). Testing was performed prior to discharge (baseline) and 4-weeks post-discharge (follow-up).ResultsRegression models showed PSQI Subjective Sleep Quality change scores from baseline to 4-week follow-up predicted a change in ADL (β = -0.22); PSQI Use of Sleep Medications change scores predicted a change in SPPB Total (β = 1.62) and SPPB Chair Stand (β = 0.63); IFS change scores predicted SPPB Total (β = -0.16) and SPPB Chair Stand performance (β = -0.07) change scores.ConclusionsFor older adults, changes in sleep medication use, daytime dysfunction, and fatigue were associated with improvements in functional recovery (including physical performance and independence) from acute hospitalization to 4-week follow-up. These results suggest that interventions focused on improving sleep quality, daytime consequences, and fatigue might help enhance physical functioning following hospitalization.Clinical trial registrationClinicalTrials.gov, identifier: NCT02203656.

Dataset Information

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

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Availability and implementation

Contact

Supplementary information

Publications

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

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