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Bio Sequence Reader

NGS related nodes for KNIME Workbench version 0.2.200.qualifier by Bernd Jagla, Institute Pasteur

Reads a sequence file into two columns: seq_name and sequence

This implementation uses the Biojava (VERSION 1.7.1) implementation for reading the data

It creates a sequence object that can be accessed by special nodes

The following file formats can be read in Fasta Genbank uniprot embl INSDseq

you also have to specify if the sequences are RNA, DNA, protein sequences

Annotations are stored with the sequence objects

Sample code to access annotation

Sample code to access sequence information

Large sequence files with lots of annotations might not fit into memory

Options

File name
Filename of sequence file
Type
Sequence type (RNA, DNA, Protein)
Format
File format (FASTA, Genbank, Uniprot, embl, INSDseq)
Limit
Limit the number of entries to read in. (0=all)

Output Ports

Icon
Sequence object representation of the input file

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install KNIME NGS tools from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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