1.6.0

SEDA v1.6.0 release. This release:

• Adds a Command-Line Interface (CLI) for all operations.
• Includes new distributions for APT (Advanced Package Tool), used in Debian-based distributions like Ubuntu or Kubuntu, RPM (Red Hat Package Manager), used in Fedora or CentOS, among others, and Snap.
• Fixes a bug when filtering by reference sequence size difference from an external file.

In addition, the SEDA pipelines with Compi project provides a framework for easily creating pipelines made up of SEDA commands using Compi.

v1.5.1

• Fixes the PfamScan operation that was not working due to changes in the web service.
• Fixes a bug in the PfamScan operation that was causing the expectation value was not submitted in the query.

v1.5.0

SEDA v1.5.0 release. This release adds support for running the CGA (Conserved Genome Annotation) Pipeline as a new Gene annotation operation.

v1.4.0

SEDA v1.4.0 release. This release fixes the Splign/Compart protocol to properly retrieve the FASTA sequences from the Splign/Compart annotations. So far, we were creating a bidirectional genome (the original genome plus its reverse-complement) but we realized that Splign/Compart is able to annotate in both strands and therefore such bidirectional genome is no longer needed. After removing this, the way that the FASTA sequences are extracted from the annotations varies depending on the query/subject start/end coordinates. This is described in the corresponding section of the manual.

v1.3.2

Fixes a bug when running BLAST operations using Docker. The bug was only affecting to BLAST commands execution in Docker that require protein databases (e.g. blastp) and use an alias (i.e. "query against all databases" was used).

v1.3.1

This release fixes an important bug in the ProSplign/ProCompart pipeline. The tblastn output must be sorted by subject and query and so far it was not being sorted properly. This commit fixes this behavior and now the output is sorted properly by subject and query as the procompart tool requires.

v1.3.0

SEDA v1.3.0 release. The main updates are:

• Fix unstable Splign/Compart behaviour.
• Allow importing patterns from FASTA files.
• Add a new consensus sequence mode.

Splign/Compart

The first step of the Splign/Compart pipeline is the creation of a bidirectional genome containing the sequences of original genome and the reverse-complement counterparts of these sequences. So far, this pipeline created two intermediante FASTA files containing the reverse-complement sequences, the renamed reverse-complement sequences, and the third and final file containing the bidirectional genome. We have observed that running Splign in a directory with other FASTA files than the tworequired inputs (the bidirectional genome and the CDS) makes it to fail to annotate genes in some environments while behaving properly on others. It seems that the presence of these additional FASTA files is a problem to Splign under some circunstances and since these files are not required they are now removed from the temporary directory created to run the Splign/Compart pipeline.

v1.2.2

This release does not include any updates on the functionality of SEDA or bug fixes. It just updates junit from 4.12 to 4.13.1

v1.2.1

This release reduces the memory usage when writing FASTA files.

v1.2.0

SEDA v1.2.0 release. The main updates are:

• Add NCBI BLAST and UniProt BLAST operations to run BLAST queries using the NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and UniProt (https://www.uniprot.org/blast/) web servers respectively.
• Add PfamScan plugin with a new operation to search and annotate sequences against the Pfam-A HMM library using the EMBL-EBI web service (https://www.ebi.ac.uk/Tools/pfa/pfamscan/)
• Parallelize the "BLAST: two-way ortholog identification" operation.
• Update manual to include step-by-step execution guides of three protocols.
• Show operation elapsed time when finished.
• Capture out of memory errors to show a warning message to users.
• Minor fixes.