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LOCARNA_P(1) User Commands LOCARNA_P(1) NAME locarna_p - manual page for locarna_p (LocARNA 2.0.0) DESCRIPTION locarna_p - pairwise partition function of RNA alignments. Computes base and base pair match probabilities from alignment partiti- tion functions. USAGE: locarna_p [options] <Input 1> <Input 2> locarna_p computes sequence and structure match probabilities from par- tition functions of locarna pairwise alignments, i.e. from fast simul- taneous folding and alignment based on two RNA sequences (or align- ments). Input and Constraints Please see the documentation of locarna for inputs and the possible constraints specifications. Output Probabilities of base and base pair matches can be written to files. (The total partition function is reported to standard out.) OPTIONS -h, --help Print this help. -V, --version Print only version string. -v, --verbose Be verbose. Prints input parameters, sequences and size informa- tion. -q, --quiet Be quiet. Scoring parameters: -i, --indel=<score>(-150) Indel score. Score contribution of each single base insertion or deletion. Indel opening score and indel score define the affine scoring of gaps. --indel-opening=<score>(-750) Indel opening score. Score contribution of opening an insertion or deletion, i.e. score for a consecutive run of deletions or insertions. Indel opening score and indel score define the affine scoring of gaps. --ribosum-file=<f>(RIBOSUM85_60) File specifying the Ribosum base and base-pair similarities. [default: use RIBOSUM85_60 without requiring a Ribosum file.] --use-ribosum=<bool>(true) Use ribosum scores for scoring base matches and base pair matches; note that tau=0 suppresses any effect on the latter. -m, --match=<score>(50) Set score contribution of a base match (unless ribosum scoring). -M, --mismatch=<score>(0) Set score contribution of a base mismatch (unless ribosum scor- ing). -s, --struct-weight=<score>(200) Maximal weight of 1/2 arc match. Balances structure vs. se- quence score contributions. -e, --exp-prob=<prob> Expected base pair probability. Used as background probability for base pair scoring [default: calculated from sequence length]. -t, --tau=<factor>(50) Tau factor. Factor for contribution of sequence similarity in an arc match (in percent). tau=0 does not penalize any sequence in- formation including compensatory mutations at arc matches, while tau=100 scores sequence similarity at ends of base matches (if a scoring matrix like ribosum is used, this adds the contributions for base pair match from the matrix). [default tau=0!] --temperature-alipf=<int>(300) Temperature for the /sequence alignment/ partition functions used by the probcons-like sequence-based match/trace probability computation (this temperature is different from the 'physical' temperature of RNA folding!). Partition function representation: --pf-scale=<scale>(1.0) Factor for scaling the partition functions. Use in order to avoid overflow. --extended-pf Use extended precision for partition function values. This in- creases run-time and space (less than 2x), however enables han- dling significantly larger instances. --quad-pf Use quad precision for partition function values. Even more pre- cision than extended pf, but usually much slower (overrides ex- tended-pf). Output: --write-arcmatch-probs=<file> Write arcmatch probabilities --write-basematch-probs=<file> Write basematch probabilities -a, --min-am-prob=<amprob>(0.001) Minimal arc match probability. Write probabilities for only the arc matchs of at least this probability. -b, --min-bm-prob=<bmprob>(0.001) Minimal base match probability. Write probabilities for only the base matchs of at least this probability. --include-am-in-bm Include arc match cases in base match probabilities --stopwatch Print run time informations. Heuristics for speed accuracy trade off: -p, --min-prob=<prob>(0.001) Minimal probability. Only base pairs of at least this probabil- ity are taken into account. --max-bps-length-ratio=<factor>(0.0) Maximal ratio of #base pairs divided by sequence length. This serves as a second filter on the "significant" base pairs. [de- fault: 0.0 = no effect]. -D, --max-diff-am=<diff>(-1) Maximal difference for sizes of matched arcs. [-1=off] -d, --max-diff=<diff>(-1) Maximal difference for positions of alignment traces (and aligned bases). [-1=off] --max-diff-at-am=<diff>(-1) Maximal difference for positions of alignment traces at arc match ends. [-1=off] --max-diff-aln=<aln file>() Maximal difference relative to given alignment (file in clustalw format) --max-diff-pw-aln=<alignment>() Maximal difference relative to given alignment (string, de- lim=AMPERSAND) --max-diff-relax Relax deviation constraints in multiple aligmnent --min-trace-probability=<probability>(1e-5) Minimal sequence alignment probability of potential traces (probability-based sequence alignment envelope) [default=1e-4]. Computed probabilities: --fragment-match-probs=<"i j k l">() Requests probabilities for the match of fragments [i..j] and [k..l]. Accepts a ';' separated list of ranges. Constraints: --maxBPspan=<span>(-1) Limit maximum base pair span [default=off]. --relaxed-anchors Use relaxed semantics of anchor constraints [default=strict se- mantics]. Input files: The tool is called with two input files <Input 1> and <Input 2>, which specify the two input sequences or input alignments. Dif- ferent input formats (Fasta, Clustal, Stockholm, LocARNA PP, Vi- ennaRNA postscript dotplots) are accepted and automatically rec- ognized (by file content); the two input files can be in differ- ent formats. Extended variants of the Clustal and Stockholm for- mats enable specifying anchor and structure constraints. DISCLAIMER locarna_p is a low level tool; most often this tool is used indirectly, by calling mlocarna with --probabilistic. Note that the performance of locarna_p (as well as basically all tools in the LocARNA package) is often significantly improved by the use of suitable application-spe- cific options, deviating from the default settings. AVAILABILITY The latest LocARNA package release is available online at at Github https://github.com/s-will/LocARNA and http://www.bioinf.uni- freiburg.de/Software/LocARNA/ COPYING (LICENSE) Copyright 2005- Sebastian Will. The LocARNA package is released under GNU Public License v3.0 REFERENCES Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen. LocARNA-P: Accurate boundary prediction and improved de- tection of structural RNAs. RNA, 18 no. 5 pp. 900-914, 2012. doi: 10.1261/rna.029041.111 EXAMPLES Please see the documentation of locarna for call and input constraint examples. AUTHOR This man page is written and maintained by Sebastian Will it is part of the LocARNA package. First versions of locarna_p and its aligner class were written by Tejal Joshi. REPORTING BUGS Report bugs to <will (at) informatik.uni-freiburg.de>. locarna_p (LocARNA 2.0.0) November 2022 LOCARNA_P(1)
NAME | DESCRIPTION | OPTIONS | DISCLAIMER | AVAILABILITY | COPYING (LICENSE) | REFERENCES | EXAMPLES | AUTHOR | REPORTING BUGS
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