Table 5 The 8 pipeline models currently available in FIGENIX

ProtPhyloGenix

The phylogenomic functional inference pipeline shown in this paper and detailed in the supplement.

TwinBaseMatix

Builds a FASTA database, eliminating redundant sequences obtained from two different query databases. For example, mixes protein coming from NR and Ensembl databases, and eliminates doubles.

BaseProtPhylogenix

Composition of the two previous pipelines. This pipeline first builds a temporary protein database (mixing two different databases and eliminating doubles). The phylogenomic inference process is then run using the built database.

TwinESTMatix

Builds a FASTA database, mixing sequences obtained on the one hand from a filtered given database and on the other hand by a database of automatically clustered ESTs. For example, it allows mixing protein coming from NR and translations of EST contigs from NCBI dbEST database.

BaseESTPhylogenix

Composition of TwinESTMatix and ProtPhyloGenix__ pipelines. Phylogenomic inference on FASTA databases built with TwinESTMatix This allows construction of phylogenetic tress mixing proteins and translated EST contigs.

GenePredix

Runs our structural annotation method (mixing ab-initio and homology information) to DNA sequence up to ~50 kb (due to current computational power limitations) to predict genes. For larger DNA sequences, SlidingGenePredix can be used.

SlidingGenePredix:

Apply the GenePredix pipeline on a sliding window. This allows gene prediction on larger DNA sequences, and bypasses the ~50 kb limitation.

PhyloGenix:

Composition of GenePredix and ProtPhyloGenix pipelines. This model allows automatic structural and functional annotation of DNA sequences. Indeed it produces gene prediction in DNA sequences using GenePredix, and then performs phylogenomic functional inference for each putative gene using ProtPhyloGenix.