# Introduction ## Presentation BeeDeeM is a general-purpose Bioinformatics Databank Manager. This manual explains how to install, configure and use *BeeDeeM*. ## Main features *BeeDeeM* automatically performs: * the handling of any set of files compliant to Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl, Fasta and Silva formats * the handling of major biological classifications (ontologies), such as NCBI Taxonomy, Gene Ontology, Enzyme, Intepro and PFAM * the download of files from remote sites (via FTP or Aspera), * the decompression of the files (gzip files), * the un-archiving of the files (tar files), * the conversion of native sequence banks (e.g. Genbank) to FASTA files, * the preparation of databanks in BLAST format from native sequence bank formats, * the indexing of Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl, Fasta and Silva files allowing their efficient querying by way of sequence identifiers, * the indexing of sequence features and ontologies data (NCBI Taxonomy, Gene Ontology, Enzyme Commission, Intepro and PFAM domains), * the preparation of taxonomic subsets out of annotated sequence banks, * the filtering of sequence banks with user-defined constraints. *Task execution extension:* * Any kind of pre- and post-processing of data can be done using external scripts * Such scripts can be executed on the host computer (local mode) or though SGE, PBS or SLURM scheduler (cluster mode) * Task executions are controlled by configuration files; *e.g.* to specify software ressources (RAM, CPU, walltime), access to softwares (direct execution or through Conda), *etc.* *Index creation extension:* * Using the task execution engine, additional index can be quite easily created in a fully automated way (e.g. Diamond, Bowtie, *etc.*) ## Main tools *BeeDeeM* provides a toolchain made of: * [a command-line tool to automate databanks installation](/beedeem/getting-started.md) * [a command-line tool to annotate BLAST results](/beedeem/utils/cmdline-annotate.md) * [a command-line to query databanks using sequence IDs](/beedeem/utils/cmdline-query.md) * [a UI front-end to do the same in a more friendly way](/beedeem/getting-started-1.md) ## Practical use cases Among others, these databanks can be used to: * prepare and maintain up-to-date local copy of usefull data * run BLAST sequence comparison jobs * annotate BLAST results with sequence features and ontologies ## Companion tools *BeeDeeM* features and data are accessible from: * [BLAST Viewer](https://github.com/pgdurand/BlastViewer) * [BioDocument Viewer](https://github.com/pgdurand/BioDocumentViewer) * [BLAST Filter Tool](https://github.com/pgdurand/BLAST-Filter-Tool) * [Plealog Bioinformatics Core API](https://github.com/pgdurand/Bioinformatics-Core-API) It is worth noting that BeeDeeM is capable of [creating Galaxy Data Manager loc files](/beedeem/utils/list-banks.md), enabling a Galaxy web portal to use banks installed by BeeBeeM. ## More about some features ### Ready for cluster BeeDeeM can be used from the command-line or from a graphical user interface. It is cluster ready: use of a job scheduler (e.g. PBS, SLURM), smooth use of cluster structures (e.g. data downloading from Internet-connected nodes vs. data processing on network-isolated nodes). ### Ready for Aspera BeeDeeM is capable of using the Aspera high speed data transfer system. In such a way, the software can quickly retrieve data from NCBI and EBI, both institutes providing Aspera servers for data retrieval. ### Annotate your BLAST results The software comes with utility tools such as databank filtering, databank querying, and BLAST/DIAMOND/PLAST annotator; banks installed by BeeDeeM being indexed, they can be used to collect features data (including ontologies) and add all that information within results of above mentioned sequence comparison tools. ### Parallel data processing engine Whatever the source of sequence files (public institutes or personal data), *BeeDeeM* converts them into (a) BLAST databanks and (b) sequence data indexes. Then, all these databanks are available for use with several ready-to-use softwares and Java API (see [Companion tools](/beedeem/master.md#companion-tools)). The conversion of sequence files into a BLAST databank is done in a fully automated way by *BeeDeeM*. While NCBI 'makeblastdb' only handles Fasta files, *BeeDeeM* is capable of converting directly Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl and Silva files into a BLAST databank in avery straightforward way. Sequence data indexes are used in various places of the software to retrieve sequence annotations given sequence identifiers. To achieve such a data retrieval task in a very effective way, the source sequence files have to come with a dictionary associating sequence identifiers to sequence data. Again, the Databank Manager is capable of creating such a dictionary automatically, whatever the format of the source sequence files. Finally, concerning public sequence databanks, BeeDeeM is capable of running in a fully automated way the retrieval of sequence files from the FTP servers of public institutes (such as NCBI, EBI, Uniprot, GeneOntology, *etc.*), as well as from your own in-house FTP servers if any are available. ## License *BeeDeeM* is a free open-source software released under the terms of: [![License AGPL](https://img.shields.io/badge/license-Affero%20GPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.txt) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://pgdurand.gitbook.io/beedeem/master.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.