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deFUME 1.0 - Dynamic Exploration of Functional Metagenomics Sequencing Data

deFUME is a web service that assembles Sanger sequencing reads, identifies ORFs and blasts these as well as annotating them with InterPro. The results are shown as an interactive web-based report in table format.

Instructions Paper abstract

SUBMISSION

Upload sequences

deFUME takes ab1 files as input, in order to upload these to the server you first need to compress them in a zip or tar.gz file yourself. Read here how to do this.

Raw sanger sequencing reads (ab1. format) compressed as zip or tar.gz.
       

Pre-assembled sequencing data


ASSEMBLED NUCLEOTIDE SEQUENCES

Cannot be used with chromatogram or vector sequence submission.
NOTE: Reads will not be shown on output visualization.

Paste a single nucleotide sequence or several sequences in FASTA format into the field below:


or upload a file in FASTA format directly from your local disk:

Load example data set.

If you don't want to run the test data but directly view the deFUME result, click here

Recommended input

PRIMER SEQUENCES

In order for deFUME to know which ab1 file is a forward and which is a reverse read you can enter a "primer pattern" below. For example if all your forward reads contain _F_ in the filename, enter that here. Separate multiple entries by comma, e.g. _OGEN41_,_F_


Forward primer pattern: Optional

Reverse primer pattern: Optional

E-MAIL ADDRESS

deFUME uses the Interpro database at EMBL-EBI and this requires a valid mail address. If you don't provide an valid e-mail address deFUME will not include any GO annotations and Interpro links, severly limiting the vizualization of your dataset

Email for InterPro queries: Optional

Advanced input


CLONING VECTOR SEQUENCE(S)

Paste a single nucleotide sequence or several sequences in FASTA format into the field below:

or upload a file in FASTA format directly from your local disk:






Base calling error rate:
Accuracy of base calls expressed as error probability.
The standard probability is 0.01, which corresponds to
a base call probability of 99% (or 1 error in 100 bases).
Optional



deFUME will check your browser automatically for compatibility, read here about the browser that were successfully tested.




CITATIONS

For publication of results, please cite:

van der Helm E, Geertz-Hansen HM, Genee HJ, Malla S, Sommer MOA: deFUME: Dynamic exploration of functional metagenomic sequencing data. BMC Res Notes 2015, 8:328




GETTING HELP

Scientific problems:        Technical problems: