Efficient high-energy Raman soliton generation in a Tm:doped large mode area fiber amplifier.

We report the Tm-doped all-fiber MOPA based on a LMA active fiber generating Raman solitons tunable in the range 1970-2300 nm directly from the LMA fiber. By tuning the chirp of the input pulse we reached more than 90 % energy transfer efficiency to Raman soliton. Solitons with 125 fs duration and up to 24 nJ energy are demonstrated in LMA fiber amplifier. We show experimentally that Raman solitons experience both amplification and absorption in active fiber components of the laser system and that the energy of a Raman soliton generated in an LMA fiber amplifier is limited by the soliton area theorem.

TIGRFAMs and Genome Properties in 2013.

TIGRFAMs, available online at http://www.jcvi.org/tigrfams is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more functionally heterogeneous families are designated subfamily or domain, and assign less specific but more widely applicable annotations. The Genome Properties database, available at http://www.jcvi.org/genome-properties, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. Both databases specialize heavily in bacterial and archaeal subsystems. At present, 4284 models appear in TIGRFAMs, while 628 systems are described by Genome Properties. Content derives both from subsystem discovery work and from biocuration of the scientific literature.