<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/42491?offset=70 https://bioinformaticsonline.com/bookmarks/view/41475/proteoclade-a-taxonomic-toolkit-for-multi-species-and-metaproteomic-analysis Wed, 18 Mar 2020 14:27:20 -0500 https://bioinformaticsonline.com/bookmarks/view/41475/proteoclade-a-taxonomic-toolkit-for-multi-species-and-metaproteomic-analysis <![CDATA[ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis]]> ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements.

ProteoClade helps you analyze two general categories of experiments:

  1. Targeted Database Searches: Experiments in which a limited number of species are defined ahead of time, such as those involving Patient-Derived Xenografts (PDXs) or host-pathogen interactions. Reference protein sequence databases are used for targeted searches (ex: using Mascot, MaxQuant).

  2. De Novo Searches: Experiments in which the organisms are unspecified ahead of time or involve samples of high taxonomic complexity. Mass spectra are analyzed in the absence of a reference database (ex: using PEAKS, PepNovo).

ProteoClade scales from two organisms to every organism in UniProt. Please refer to the complete documentation at proteoclade.readthedocs.io for installation, a user's guide, and examples.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007741

Address of the bookmark: https://github.com/HeldLab/ProteoClade

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39898/itis-the-integrated-taxonomic-information-system Fri, 30 Aug 2019 23:07:15 -0500 https://bioinformaticsonline.com/bookmarks/view/39898/itis-the-integrated-taxonomic-information-system <![CDATA[ITIS: the Integrated Taxonomic Information System!]]> ITIS, the Integrated Taxonomic Information System! Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. We are a partnership of U.S., Canadian, and Mexican agencies (ITIS-North America); other organizations; and taxonomic specialists. ITIS is also a partner of Species 2000 and the Global Biodiversity Information Facility (GBIF). The ITIS and Species 2000 Catalogue of Life (CoL)partnership is proud to provide the taxonomic backbone to the Encyclopedia of Life (EOL). 

https://www.itis.gov/pdf/twb_ug.pdf

Address of the bookmark: https://www.itis.gov/

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