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Extraction of ORFs from PASA assemblies (auto-annotation and/or reference ORFs for training gene predictors)

OpenSans Regular. One Architecture.
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We use density functional theory as implemented in the Vienna Ab Initio Simulation Package (VASP) software to evaluate the total energy of compounds. For the exchange-correlational functional, we employ a mix of Generalized Gradient Approximation (GGA) and GGA+U, as described later in this manual. We use the Projector Augmented Wave (PAW) method for modeling core electrons with an energy cutoff of 520 eV.
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The PASA alignment assemblies can be used to automatically extract protein coding regions to be used for automated transcript-based genome annotation and/or for generating a high quality data set for training ab initio gene predictors (ex. Augustus, SNAP, genemarkHMM, glimmerHMM, etc.). Our TransDecoder software, bundled with PASA, is used to identify likely coding regions.

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After running the PASA to assemble all transcript alignments as described above, you can run the following.

Run the following from your PASA working directory. The example below is what I would run in the sample_data/ directory:

This should generate a series of files, described below:

'fasta.transdecoder.cds,.pep,.gff3,.bed' :correspond to likely coding regions found in the PASA assemblies, coordinates based on the transcripts and not the genome.
'fasta.transdecoder.genome.bed,gff3' :coordinates of gene models based on the genome sequence.

The 'fasta.transdecoder.pep' file has headers like so:

The accession corresponds to the PASA assembly. The type indicator can be any of the following: complete, 5prime_partial, 3prime_partial, or internal. The 5prime_partial are missing a start codon and translate to the very 5' end, 3prime_partial are missing a stop codon and translate to their very 3' end, and internal translate from the first to the last basepair in the sequence, missing a start and a stop codon. The 'complete' category are of greatest interest for the prospects of ab initio genefinder training. Typically, we would search these complete proteins against the non-redundant protein database at GenBank and identify those ORFs that have good database matches across most of their length. Such entries can be confidently used for training, in addition to those particularly long ORFs that do not match known proteins and are sufficiently complex in sequence.

(Redirected from Ab Initio)

Ab initio (/ˌæbɪˈnɪʃi.oʊ/AB-i-NISH-ee-oh)^[1] is a Latin term meaning 'from the beginning' and is derived from the Latin ab ('from') + initio, ablativesingular of initium ('beginning').

2Uses

Etymology[edit]

c. 1600, from L., lit. 'from the beginning', from ablative case of initium 'entrance, beginning', related to verb inire 'to go into, enter upon, begin'.^[2]

Uses[edit]

Ab initio (abbreviation: ab init.) is used in several contexts, including the following:

Law[edit]

In law, ab initio refers to something being the case from the start or from the instant of the act rather than from when the court declared it so. For instance, the term 'void ab initio' means 'to be treated as invalid from the outset.' E.g., in many jurisdictions, if a person signs a contract under duress, that contract is treated as being 'void ab initio'.

Typically, documents or acts which are voidab initio cannot be fixed and if a jurisdiction, a document or an act is so declared at law to be void ab initio, the parties are returned to their respective positions that they were at the beginning of the event.

'Void ab initio' is often contrasted with 'voidable', such documents which become void only as of the date of the judicial declaration to that effect.

An insurer facing a claim from an insured who had deceived the insurer on a material fact would claim that the insurance contract was void ab initio; it was null and void from the beginning and that since there was no legally enforceable contract, the insurer ought not to have to pay.^[3]

Science and engineering[edit]

Documentation of a process is said to be ab initio (or from scratch, or from the ground up) if the documentation shows how to set up and complete the process from basic materials (to which a competent practitioner is expected to have access) without prior special preparation.
A calculation is said to be ab initio (or 'from first principles') if it relies on basic and established laws of nature without additional assumptions or special models. For example, an ab initio calculation of the properties of liquid water might start with the properties of the constituent hydrogen and oxygen atoms and the laws of electrostatics and quantum mechanics. From these basics, the properties of isolated individual water molecules would be derived, followed by computations of the interactions of larger and larger groups of water molecules, until the bulk properties of water had been determined.
In chemistry, an abbreviation referring to ab initio quantum chemistry methods.
Ab initio methods in nuclear physics.
In biophysics, a method for the prediction of protein structures in protein folding.
In aviation, the very first stage of flight training.
In bioinformatics, ab initio is a method for making predictions about biological features using only a computational model without extrinsic comparison to existing data. In this context, it may be sometimes interchangeable with the Latin term de novo.

Other uses[edit]

What Is Ab Initio

when describing literature, it is told from the beginning as opposed to in medias res (meaning starting in the middle of the story)
when describing a subject or a module, say when a person is learning French from the beginning, they are said to be a student of French ab initio
in language didactics, foreign languages may be studied ab initio, meaning that the course is designed for students with no previous knowledge.