Build and map profile Hidden Markov Models for Terminal Inverted Repeat families (TIR-pHMMs) to genomic sequences for annotation of MITES and complete DNA-Transposons with variable internal sequence composition.
TIRmite is packaged with tSplit a tool for extraction of terminal repeats from complete transposons.
TIRmite will use profile-HMM models of Terminal Inverted Repeats (TIRs) for genome-wide annotation of TIR families. These can be provided by the user or built from aligned TIRs oriented as 5' outer edge --> 3' inner edge.
Three classes of output are produced:
- All significant TIR hit sequences written to fasta (per query HMM).
- Candidate elements comprised of paired TIRs are written to fasta (per query HMM).
- Genomic annotations of candidate elements and, optionally, TIR hits (paired and unpaired) are written as a single GFF3 file.
- Use nhmmer genome with TIR-pHMM.
- Import all hits below --maxeval threshold.
- For each significant TIR match identify candidate partners, where:
* Is on the same sequence.
* Hit is in complementary orientation.
* Distance is <= --maxdist.
* Hit length is >= model length * --mincov. - Rank candidate partners by distance downstream of positive-strand hits, and upstream of negative-strand hits.
- Pair reciprocal top candidate hits.
- For unpaired hits, find first unpaired candidate partner and check for reciprocity.
- If the first unpaired candidate is non-reciprocal, check for 2nd-order reciprocity (is outbound top-candidate of current candidate reciprocal.)
- Iterate steps 6-7 until all TIRs are paired OR number of iterations without new pairing exceeds --stableReps.
TIRmite requires Python >= v3.8
Dependencies:
- TIR-pHMM build and search
- Extract terminal repeats from predicted TEs
You can create a Conda environment with these dependencies using the YAML files in this repo.
conda env create -f environment.yml
conda activate tirmiteNote: If you are using a Mac with an ARM64 (Apple Silicon) processor, BLAST is not currently available from Bioconda for this architecture. You can instead create a virtual OSX64 env like this:
conda env create -f env_osx64.yml
conda activate tirmite-osx64Installation options:
pip install the latest development version directly from this repo.
% pip install git+https://github.com/Adamtaranto/TIRmite.gitInstall latest release from PyPi.
% pip install tirmiteInstall from Bioconda.
% conda install -c bioconda tirmiteTest installation.
# Print version number and exit.
% tirmite --version
tirmite 1.1.6
# Get usage information
% tirmite --helpReport all hits and valid pairings of TIR_A in target.fasta (interval <= 10000, hits cover > 40% len of hmm model), and write GFF3 annotation file.
% tirmite --genome target.fasta --hmmFile TIR_A.hmm --gffOut TIR_elements_in_Target.gff3 --maxdist 10000 --mincov 0.4If you don't have a HMM of your TIR, TIRmite can create one for you using an aligned sample of your TIR with --alnFile.
To skip HMM search and run the pairing algorithm on a custom set of TIR hits (i.e. from blastn), you can provide hits in BED format with --pairbed.
TIRs should always be oriented 5`- 3` with the lefthand TIR.
In this example the two TIRs should be oriented to begin with "GA".
5` GA>>>>>>> ATGC <<<<<<<TC 3`
3` CT>>>>>>>> TACG <<<<<<<AG 5`
Run tirmite --help to view the program's most commonly used options:
tirmite [-h] [--version] --genome GENOME [--hmmDir HMMDIR]
[--hmmFile HMMFILE] [--alnDir ALNDIR] [--alnFile ALNFILE]
[--alnFormat {clustal,fasta,nexus,phylip,stockholm}]
[--pairbed PAIRBED] [--stableReps STABLEREPS] [--outdir OUTDIR]
[--prefix PREFIX] [--nopairing] [--gffOut]
[--reportTIR {None,all,paired,unpaired}] [--padlen PADLEN]
[--keeptemp] [-v] [--cores CORES] [--maxeval MAXEVAL]
[--maxdist MAXDIST] [--nobias] [--matrix MATRIX]
[--mincov MINCOV] [--hmmpress HMMPRESS] [--nhmmer NHMMER]
[--hmmbuild HMMBUILD]
Info:
-h, --help Show this help message and exit
--version Show program's version number and exit
Input options:
--genome Path to target genome that will be queried with HMMs.
Note: Sequence names must be unique. (required)
--hmmDir Directory containing pre-prepared TIR-pHMMs.
--hmmFile Path to single TIR-pHMM file. Incompatible with "--hmmDir".
--alnDir Path to directory containing only TIR alignments to be
converted to HMM.
--alnFile Provide a single TIR alignment to be converted to HMM.
Incompatible with "--alnDir".
--alnFormat Alignments provided with "--alnDir" or "--alnFile" are
all in this format.
Choices=["clustal","fasta","nexus","phylip", "stockholm"]
--pairbed If set TIRmite will preform pairing on TIRs from
custom bedfile only.
Pairing heuristics:
--stableReps Number of times to iterate pairing procedure when no
additional pairs are found AND remaining unpaired hits > 0.
(Default = 0)
Output and housekeeping:
--outdir OUTDIR All output files will be written to this directory.
--prefix PREFIX Add prefix to all TIRs and Paired elements detected in
this run. Useful when running same TIR-pHMM against
many genomes.
(Default = None)
--nopairing If set, only report TIR-pHMM hits. Do not attempt
pairing.
(Default = False)
--gffOut If set report features as prefix.gff3. File saved to
outdir.
(Default = False)
--reportTIR Options for reporting TIRs in GFF annotation file.
Choices=[None,'all','paired','unpaired']
(Default = 'all')
--padlen Extract x bases either side of TIR when writing TIRs to fasta.
(Default = None)
--keeptemp If set do not delete temp file directory.
(Default = False)
-v, --verbose Set syscall reporting to verbose.
HMMER options:
--cores Set number of cores available to hmmer software.
--maxeval Maximum e-value allowed for valid hit.
(Default = 0.001)
--maxdist Maximum distance allowed between TIR candidates to
consider valid pairing.
(Default = None)
--nobias Turn OFF bias correction of scores in nhmmer.
(Default = False)
--matrix Use custom DNA substitution matrix with nhmmer.
--mincov Minimum valid hit length as prop of model length.
(Default = 0.5)
Non-standard HMMER paths:
--hmmpress Set location of hmmpress if not in PATH.
--nhmmer Set location of nhmmer if not in PATH.
--hmmbuild Set location of hmmbuild if not in PATH.
nhmmer can be supplied with custom DNA score matrices for assessing hmm match scores. Standard NCBI-BLAST matrices such as NUC.4.4 are compatible. (See: ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/NUC.4.4)
Extract Terminal Inverted Repeats (TIRs) DNA transposons.
tSplit attempts to identify terminal repeats in transposable elements by first aligning each element to itself using nucmer, and then applying a set of tuneable heuristics to select an alignment pair most likely to represent a TIR.
- Exclude all diagonal/self-matches
- If tsplit-TIR: Retain only alignment pairs on opposite strands (inverse repeats)
- Retain pairs for which the 5' match begins within x bases of element start and whose 3' match ends within x bases of element end
- Exclude alignment pairs which overlap (potential SSRs)
- If multiple candidates remain select alignment pair with largest internal segment (i.e. closest to element ends)
For each element in dna-transposons.fasta split into internal and external (TIR) segments. Split segments will be written to TIR_split_TE-splitter_output.fasta with suffix "_I" for internal or "_TIR" for external segments. TIRs must be at least 10bp in length and share 80% identity and occur within 10bp of each end of the input element. Additionally, synthetic MITEs will be constructed by concatenation of left and right TIRs, with internal segments excised.
% tsplit-TIR -i dna-transposons.fasta -p TIR_splitRun tsplit-TIR --help to view the programs' most commonly used
options:
Usage: tsplit-TIR [-h] -i INFILE [-p PREFIX] [-d OUTDIR]
[--splitmode {all,split,internal,external,None}]
[--makemites] [--keeptemp] [-v] [-m MAXDIST]
[--minid MINID] [--minterm MINTERM] [--minseed MINSEED]
[--diagfactor DIAGFACTOR] [--method {blastn,nucmer}]
Help:
-h, --help Show this help message and exit.
Input:
-i, --infile Multifasta containing complete elements.
(Required)
Output:
-p, --prefix All output files begin with this string. (Default:[infile basename])
-d, --outdir Write output files to this directory. (Default: cwd)
--keeptemp If set do not remove temp directory on completion.
-v, --verbose If set, report progress.
Report settings:
--splitmode Options: {all,split,internal,external,None}
all = Report input sequence as well as internal and external segments.
split = Report internal and external segments after splitting.
internal = Report only internal segments.
external = Report only terminal repeat segments.
None = Only report synthetic MITES (when --makemites is also set).
(Default: split)
--makemites Experimental function: Attempt to construct synthetic MITE sequences from TIRs by concatenating
5' and 3' TIRs. Available only in 'tsplit-TIR' mode
Alignment settings:
--method Select alignment tool. Note: blastn may perform better on very short high-identity TRs,
while nucmer is more robust to small indels.
Options: {blastn,nucmer}
(Default: nucmer)
--minid Minimum identity between terminal repeat pairs. As float.
(Default: 80.0)
--minterm Minimum length for a terminal repeat to be considered.
Equivalent to nucmer "--mincluster"
(Default: 10)
-m, --maxdist Terminal repeat candidates must be no more than this many bases from ends of an input element.
Note: Increase this value if you suspect that your element is nested within some flanking sequence.
(Default: 10)
--minseed Minimum length of a maximal exact match to be included in final match cluster.
Equivalent to nucmer "--minmatch".
(Default: 5)
--diagfactor Maximum diagonal difference factor for clustering of matches within nucmer,
i.e. diagonal difference / match separation
(default 0.20)
Note: Increase value for greater tolerance of indels between terminal repeats.
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Software provided under MIT license.