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companion.sanger.ac.uk

Companion

Easy and reliable parasite genome annotation. Or find your job by ID:. Annotation of a new genome could be as easy as uploading your scaffold sequences (FASTA, EMBL, GenBank), choosing a reference (from our set of 61 species. And pushing a button! The pipeline spans many aspects of new genome production, from pseudochromosome contiguation, structural and functional gene annotation over comparative analyses to visualization. Annotation results are provided in validated GFF3. Format for GO associations.

http://companion.sanger.ac.uk/

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Companion | companion.sanger.ac.uk Reviews
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Easy and reliable parasite genome annotation. Or find your job by ID:. Annotation of a new genome could be as easy as uploading your scaffold sequences (FASTA, EMBL, GenBank), choosing a reference (from our set of 61 species. And pushing a button! The pipeline spans many aspects of new genome production, from pseudochromosome contiguation, structural and functional gene annotation over comparative analyses to visualization. Annotation results are provided in validated GFF3. Format for GO associations.
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2 submit job
3 getting started
4 example results
5 annotate your
6 sequence
7 easy
8 full stack
9 standards compliant
10 quick
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Companion | companion.sanger.ac.uk Reviews

https://companion.sanger.ac.uk

Easy and reliable parasite genome annotation. Or find your job by ID:. Annotation of a new genome could be as easy as uploading your scaffold sequences (FASTA, EMBL, GenBank), choosing a reference (from our set of 61 species. And pushing a button! The pipeline spans many aspects of new genome production, from pseudochromosome contiguation, structural and functional gene annotation over comparative analyses to visualization. Annotation results are provided in validated GFF3. Format for GO associations.

INTERNAL PAGES

companion.sanger.ac.uk companion.sanger.ac.uk
1

Submit new Companion job

https://companion.sanger.ac.uk/jobs/new

Submit a new annotation job. Step 1: Basic job properties. First of all, please specify a free-text name. For your new job. It should reflect the purpose of your job, and should probably include the organism you are annotating. Example: My new species annotation. Please also give a short species prefix. That will be used to name entities (such as genes, pseudochromosomes, etc.) generated during the annotation run. It should not contain spaces or special characters. Finally, please provide a species name.

2

Getting started with Companion

https://companion.sanger.ac.uk/getting_started

The Companion service requires input data to be in valid FASTA, GenBank or EMBL format. In files containing both annotations and sequences (such as EMBL and GenBank), only sequences will be considered. Any already existing annotation will be discarded and not included in the final result. Some additional requirements to consider:. The maximal allowed size of an uploaded file is 64 MB. The maximal allowed number of individual sequences (e.g. scaffolds) in the uploaded file is 3000. Then genes in your anno...

3

Companion example

https://companion.sanger.ac.uk/examples

This page contains some example results from a previously prepared Companion. Annotation run. The tabs below display live data and behave exactly like an actual job result page (in fact, they are the result of an actual job. That was run about 1 year ago! Click the tabs to see what data they contain. Number of annotated regions/sequences. Number of coding genes. Number of genes with function. Number of non-coding genes. Number of genes with multiple CDSs. Pseudochromosome level genomic sequence. These cl...

4

Companion FAQ

https://companion.sanger.ac.uk/faq

Can I upload large genomes? The current limit for uploaded files is 64MB. If you need to annotate input genomes larger than that, it makes sense to run a stand-alone version of Companion. On a sufficiently powerful machine, as it hits the limit of this web server. You can find the standalone version of Companion. Please follow the instructions there to set up your stand-alone instance. What species are offered as references? We import annotated parasite genomes from external sources like GeneDB. You can ...

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schistodb.net schistodb.net

SchistoDB : The Schistosoma Genomics Resource

http://schistodb.net/schisto/queries_tools.jsp;jsessionid=9E0E8732FD18C5146D05587B20AF4BE4

Publications on EuPathDB sites. Submitting data to SchistoDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Extent of Gene Overlap. Search for Metabolic Pathways. Text (synonym, InChI, etc.). View all available searches. Searches via Web Services.

fungidb.org fungidb.org

Search for Genes by Gene ID(s)

http://fungidb.org/fungidb/showQuestion.do?questionFullName=GeneQuestions.GeneByLocusTag

Publications on EuPathDB sites. Submitting data to FungiDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Text (search product name, notes, submitter etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Differences Within a Group of Isolates. Differences Between Two Groups of Isolates. The ID...

giardiadb.org giardiadb.org

Search for Genes by Gene ID(s)

http://giardiadb.org/giardiadb/showQuestion.do?questionFullName=GeneQuestions.GeneByLocusTag

Publications on EuPathDB sites. Submitting data to GiardiaDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Mass Spec. Evidence. Text (search product name, notes, submitter etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Extent of Gene Overlap. Search for SAGE Tags. New Data Sets page!

giardiadb.org giardiadb.org

GiardiaDB : The Giardia Genomics Resource

http://giardiadb.org/giardiadb/showApplication.do

Publications on EuPathDB sites. Submitting data to GiardiaDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Mass Spec. Evidence. Text (search product name, notes, submitter etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Extent of Gene Overlap. Search for SAGE Tags. New Data Sets page!

fungidb.org fungidb.org

FungiDB :: Data Submission

http://fungidb.org/fungidb/dataSubmission.jsp

Publications on EuPathDB sites. Submitting data to FungiDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Text (search product name, notes, submitter etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Differences Within a Group of Isolates. Differences Between Two Groups of Isolates. High T...

fungidb.org fungidb.org

FungiDB: The Fungal and Oomycete Genomics Resource

http://fungidb.org/fungidb/categoryPage.jsp?record=GeneRecordClasses.GeneRecordClass&category=other_attributes

Publications on EuPathDB sites. Submitting data to FungiDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Text (search product name, notes, submitter etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Differences Within a Group of Isolates. Differences Between Two Groups of Isolates. Only a...

fungidb.org fungidb.org

FungiDB: The Fungal and Oomycete Genomics Resource

http://fungidb.org/fungidb/app/answer/DatasetQuestions.AllDatasets

Publications on EuPathDB sites. Submitting data to FungiDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Text (search product name, notes, submitter etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Differences Within a Group of Isolates. Differences Between Two Groups of Isolates. Genome...

fungidb.org fungidb.org

FungiDB: The Fungal and Oomycete Genomics Resource

http://fungidb.org/fungidb/showApplication.do

Publications on EuPathDB sites. Submitting data to FungiDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Text (search product name, notes, submitter etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Differences Within a Group of Isolates. Differences Between Two Groups of Isolates. When a...

fungidb.org fungidb.org

FungiDB :: Analysis Tools

http://fungidb.org/fungidb/analysisTools.jsp

Publications on EuPathDB sites. Submitting data to FungiDB. How to submit data to us. EuPathDB Data Submission and Release Policies. How to cite us. Publications that Use our Resources. EuPathDB Brochure in Chinese. NCBI's Glossary of Terms. Text, IDs, Organism. Text (product name, notes, etc.). Text (search product name, notes, submitter etc.). Search for Genomic Sequences. Search for Genomic Segments (DNA Motif). Differences Within a Group of Isolates. Differences Between Two Groups of Isolates. When t...

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Companion

Easy and reliable parasite genome annotation. Or find your job by ID:. Annotation of a new genome could be as easy as uploading your scaffold sequences (FASTA, EMBL, GenBank), choosing a reference (from our set of 61 species. And pushing a button! The pipeline spans many aspects of new genome production, from pseudochromosome contiguation, structural and functional gene annotation over comparative analyses to visualization. Annotation results are provided in validated GFF3. Format for GO associations.

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