esl-translate - Man Page

esl-translate [options] seqfile

Given a seqfile containing DNA or RNA sequences, esl-translate outputs a six-frame translation of them as individual open reading frames in FASTA format.

By default, only open reading frames greater than 20aa are reported.  This minimum ORF length can be changed with the -l option.

By default, no specific initiation codon is required, and any amino acid can start an open reading frame. This is so esl-translate may be used on sequence fragments, eukaryotic genes with introns, or other cases where we do not want to assume that ORFs are complete coding regions. This behavior can be changed. With the -m option, ORFs start with an initiator AUG Met. With the -M option, ORFs start with any of the initiation codons allowed by the genetic code. For example, the "standard" code (NCBI transl_table 1)  allows AUG, CUG, and UUG as initiators. When -m or -M are used, an initiator is always translated to Met (even if the initiator is something like UUG or CUG that doesn't encode Met as an elongator).

If seqfile is - (a single dash), input is read from the stdin pipe. This (combined with the output being a standard FASTA file) allows esl-translate to be used in command line incantations. If seqfile ends in .gz, it is assumed to be a gzip-compressed file, and  Easel will try to read it as a stream from gunzip -c.

The output FASTA name/description line contains information about the source and coordinates of each ORF. Each ORF is named orf1, etc., with numbering starting from 1, in order of their start position on the top strand followed by the bottom strand.  The rest of the FASTA name/desc line contains 4 additional fields, followed by the description of the source sequence:

source=<s>

<s> is the name of the source DNA/RNA sequence.

coords=start..end

Coords, 1..L, for the translated ORF in a source DNA sequence of length L. If start is greater than end, the ORF is on the bottom (reverse complement) strand. The start is the first nucleotide of the first codon; the end is the last nucleotide of the last codon. The stop codon is not included in the coordinates (unlike in CDS annotation in GenBank, for example.)

length=<n>

Length of the ORF in amino acids.

frame=<n>

Which frame the ORF is in. Frames 1..3 are the top strand; 4..6 are the bottom strand. Frame 1 starts at nucleotide 1. Frame 4 starts at nucleotide L.

By default, the "standard" genetic code is used (NCBI transl_table 1).  Any NCBI genetic code transl_table can be selected with the -c option, as follows:

1

Standard

2

Vertebrate mitochondrial

3

Yeast mitochondrial

4

Mold, protozoan, coelenterate mitochondrial; Mycoplasma/Spiroplasma

5

Invertebrate mitochondrial

6

Ciliate, dasycladacean, Hexamita nuclear

9

Echinoderm and flatworm mitochondrial

10

Euplotid nuclear

11

Bacterial, archaeal; and plant plastid

12

Alternative yeast

13

Ascidian mitochondrial

14

Alternative flatworm mitochondrial

16

Chlorophycean mitochondrial

21

Trematode mitochondrial

22

Scenedesmus obliquus mitochondrial

23

Thraustochytrium mitochondrial

24

Pterobranchia mitochondrial

25

Candidate Division SR1 and Gracilibacteria

As of this writing, more information about the genetic codes in the NCBI translation tables is at http://www.ncbi.nlm.nih.gov/Taxonomy/ at a link titled Genetic codes.

DNA sequences may contain IUPAC degeneracy codes, such as N, R, Y, etc. If all codons consistent with a degenerate codon translate to the same amino acid (or to a stop), that translation is done; otherwise, the codon is translated as X (even if one or more compatible codons are stops). For example, in the standard code, UAR translates to * (stop), GGN translates to G (glycine), NNN translates to X, and UGR translates to X (it could be either a UGA stop or a UGG Trp).

Degenerate initiation codons are handled essentially the same. If all codons consistent with the degenerate codon are legal initiators, then the codon is allowed to initiate a new ORF. Stop codons are never a legal initiator (not only with -m or -M but also with the default of allowing any amino acid to initiate), so degenerate codons consistent with a stop cannot be initiators. For example, NNN cannot initiate an ORF, nor can UGR -- even though they translate to X. This means that we don't translate long stretches of N's as long ORFs of X's, which is probably a feature, given the prevalence of artificial runs of N's in genome  sequence assemblies.

Degenerate DNA codons are not translated to degenerate amino acids other than X, even when that is possible. For example, SAR and MUH are decoded as X, not Z (Q|E) and J (I|L). The extra complexity needed for a degenerate to degenerate translation doesn't seem worthwhile.

-h

Print brief help. Includes version number and summary of all options.  Also includes a list of the available NCBI transl_tables and their numerical codes, for the -c option.

-c <id>

Choose alternative genetic code <id> where <id> is the numerical code of one of the NCBI transl_tables.

-l <n>

Set the minimum reported ORF length to <n> aa.

-m

Require ORFs to start with an initiator codon AUG (Met).

-M

Require ORFs to start with an initiator codon, as specified by the allowed initiator codons in the NCBI transl_table. In the default Standard code, AUG, CUG, and UUG are allowed as initiators. An  initiation codon is always translated as Met, even if it does not normally encode Met as an elongator.

-W

Use a memory-efficient windowed sequence reader. The default is to read entire DNA sequences into memory, which may become memory limited for some very large eukaryotic chromosomes. The windowed reader cannot  reverse complement a nonrewindable input stream, so  either seqfile must be a file, or you must use --watson to limit translation to the top strand.

--informat <s>

Assert that input seqfile is in format <s>, bypassing format autodetection. Common choices for <s> include: fasta, embl, genbank. Alignment formats also work; common choices include: stockholm, a2m, afa, psiblast, clustal, phylip. For more information, and for codes for some less common formats, see main documentation. The string <s> is case-insensitive (fasta or FASTA both work).

--watson

Only translate the top strand.

--crick

Only translate the bottom strand.

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Copyright (C) 2020 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.

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