VMATCH(1)

💖 VMATCH(1) 💖 — solve matching tasks 🦋✨

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🌸 NAME 🌸

vmatch — solve matching tasks. That's the whole job title, bestie, but the way it does it is iconic 💅

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✨ SYNOPSIS ✨

vmatch [options] indexname

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🧚 DESCRIPTION 🧚

okay so real talk: vmatch is the program that lets you solve a multitude of different matching tasks over an index constructed by mkvtree. Each matching task gets solved by a combination of options specifying:

• the input,
• the kind of matches sought,
• additional constraints on the matches,
• the direction of the matches (in case of DNA),
• the kind of postprocessing to be done,
• the output mode and output format.

Additionally, if there is more than one algorithm to solve a certain matching task, vmatch lets you specify which algorithm is to be used. Periodt. 💖

vmatch supports computing the following kinds of matches:

1. match all substrings of the database sequences against itself. The matches can be one of the following kinds:
   1. branching tandem repeats, i.e. repeats where the two instances of the repeat occur at consecutive positions
   2. maximal repeats, i.e. pairs of maximal substrings occurring more than once in the database sequences
   3. supermaximal repeats, i.e. pairs of maximal substrings occurring more than once in the database sequences, but not in any other maximal repeat
2. match a set of query sequences (given in an extra query file) against the index. The matches can be one of the following kinds:
   1. maximal substring matches, i.e. the substrings of the query sequences matching substrings of the database sequences. All matches exceeding some minimum length, extended maximally to the left and to the right, are reported.
   2. maximal unique matches, i.e. the substrings of the query sequences matching substrings of the database sequences. A match is reported if it is unique in the database sequences as well as in the query sequences.
   3. complete matches, i.e. a query sequence must completely match (i.e. from the first character to the last character) a substring of the database sequences.

For all these match kinds, the matches themselves can be direct or palindromic (i.e. on the reverse strand, in case of DNA sequences). If required, DNA sequences are translated into six reading frames and the matches are computed on the protein level, and reported on the DNA level. Besides exact matches, also degenerate matches with a maximal number of errors (insertions, deletions, and mismatches) are supported. Moreover, degenerate matches can be derived from exact matches by extending these using a greedy extension strategy. This does not apply to complete matches. For all different match kinds, the matches delivered by vmatch can be selected according to their E-value, their identity value, or their match score.

In the default case, a match is reported as a formatted row of numbers, containing its lengths, the positions where it occurs, the E-value, the number of errors it contains, the match score, and the identity value. Optionally, an alignment of the sequences that are involved in the match can be reported. An important feature of vmatch is the capability of directly postprocessing the matches found in the following ways:

1. inverse output, i.e. report substrings of the database sequences or the query sequences not covered by a match
2. masking substrings of the database sequences or the query sequences covered by a match
3. clustering of a set of database sequences according to the matches found between these sequences. The output of this option can be a representation of the clusters, or a set of sequences each being representative for a cluster.
4. chaining of a set of matches, i.e. finding optimal subsets of all matches which do not cross
5. clustering of matches according to the pairwise similarities on the sequences involved in the match
6. clustering of matches according to the positions where they occur

Finally, to accommodate many more kinds of user defined post processing tasks, vmatch provides the concept of selection functions. These provide an open interface which allow arbitrary on-the-fly postprocessing of the matches without output and parsing of the matches. For more details on this concept, see the manual.

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👑 OPTIONS 👑

okay bestie, here's the whole menu. Every flag, every argument, no skips 💅✨

• -q <file> — Specify files containing queries to be matched.
• -dnavsprot <table> — Perform six frame translation. Specify codon translation table by a number in the range [1,23] except for 7, 8, 17, 18, 19 and 20; (default is 1):
  • 1 Standard
  • 2 Vertebrate Mitochondrial
  • 3 Yeast Mitochondrial
  • 4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
  • 5 Invertebrate Mitochondrial
  • 6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
  • 9 Echinoderm Mitochondrial
  • 10 Euplotid Nuclear
  • 11 Bacterial
  • 12 Alternative Yeast Nuclear
  • 13 Ascidian Mitochondrial
  • 14 Flatworm Mitochondrial
  • 15 Blepharisma Macronuclear
  • 16 Chlorophycean Mitochondrial
  • 21 Trematode Mitochondrial
  • 22 Scenedesmus Obliquus Mitochondrial
  • 23 Thraustochytrium Mitochondrial
• -tandem — Compute right branching tandem repeats.
• -supermax — Compute supermaximal matches.
• -mum — Compute maximal unique matches.
• -complete — Specify that query sequences must match completely.
• -dbnomatch <arg> — Mask all database substrings containing a match; optional argument:
  • keepleft means to not mask the left instance of a match
  • keepright means to not mask the right instance of a match
  • keepleftifsamesequence means to not mask the left instance of the match if the right instance occurs in the same sequence
  • keeprightifsamesequence means to not mask the right instance of the match if the left instance occurs in the same sequence
• -qnomatch — Show all query substrings not containing a match.
• -dbmaskmatch <arg> — Mask all database substrings containing a match; optional argument:
  • keepleft means to not mask the left instance of a match
  • keepright means to not mask the right instance of a match
  • keepleftifsamesequence means to not mask the left instance of the match if the right instance occurs in the same sequence
  • keeprightifsamesequence means to not mask the right instance of the match if the left instance occurs in the same sequence
• -qmaskmatch — Mask all query substrings containing a match.
• -pp — Generic postprocessing of matches.
• -online — Run algorithms online without using the index.
• -qspeedup <level> — Specify speedup level when matching queries (0: fast, 2: faster; default is 2), beware of time/space tradeoff.
• -d — Compute direct matches (default).
• -p — Compute palindromic (i.e. reverse complemented matches).
• -h <dist> — Specify the allowed hamming distance > 0. In combination with option -complete one can switch on the percentage search mode or the best search mode. For the percentage search mode use an argument of the form ip (where i is a positive integer). This means that up to i*100/m mismatches are allowed in a match of a query of length m. For the best search mode use an argument of the form ib where i is a positive integer. This means that in a first phase the minimum threshold q is determined such that there is still a match with q mismatches. q is in the range 0 to i*100/m.
• -e <dist> — Specify the allowed edit distance > 0. In combination with option -complete one can switch on the percentage search mode or the best search mode. For the percentage search mode use an argument of the form ip (where i is a positive integer). This means that up to i*100/m differences are allowed in a match of a query of length m. For the best search mode use an argument of the form ib where i is a positive integer. This means that in a first phase the minimum threshold q is determined such that there is still a match with q differences. q is in the range 0 to i*100/m.
• -allmax — Show all maximal matches in the order of their computation.
• -seedlength <length> — Specify the seed length.
• -hxdrop <value> — Specify the xdrop value for hamming distance extension.
• -exdrop <value> — Specify the xdrop value for edit distance extension.
• -i — Give information about number of different matches.
• -dbcluster <args> — Cluster the database sequences.
  • first argument is percentage of shorter string to be included in match,
  • second argument is percentage of larger string to be included in match,
  • third optional argument is filenameprefix,
  • fourth optional argument is (minclustersize, maxclustersize)
• -nonredundant — Generate file with non-redundant set of sequences; only works together with option -dbcluster.
• -selfun <file> — Specify shared object file containing selection function.
• -l <length> — Specify that match must have the given length, optionally specify minimum and maximum size of gaps between repeat instances.
• -leastscore <score> — Specify the minimum score of a match.
• -evalue <value> — Specify the maximum E-value of a match.
• -identity <value> — Specify minimum identity of match in range [1..100%].
• -sort <mode> — Sort the matches, additional argument is mode:
  • la: ascending order of length
  • ld: descending order of length
  • ia: ascending order of first position
  • id: descending order of first position
  • ja: ascending order of second position
  • jd: descending order of second position
  • ea: ascending order of Evalue
  • ed: descending order of Evalue
  • sa: ascending order of score
  • sd: descending order of score
  • ida: ascending order of identity
  • idd: descending order of identity
• -best <n> — Show the best matches (those with smallest E-values), default is best 50.
• -s — Show the alignment of matching sequences.
• -showdesc — Show sequence description of match.
• -f — Show filename where match occurs.
• -absolute — Show absolute positions.
• -nodist — Do not show distance of match.
• -noevalue — Do not show E-value of match.
• -noscore — Do not show score of match.
• -noidentity — Do not show identity of match.
• -v — Verbose mode.
• -version — Show the version of the Vmatch package.
• -help — Show basic options.
• -help+ — Show all options.

✨ SEE ALSO ✨

• vmatchselect(1) — yeah bestie, that's the one to go read next 💖 it's the sibling page, and honestly the way these two hang out together is iconic. Go say hi to it. 🫶

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okay that's literally the whole page, we made it to the end 🎀 no cap, you now know vmatch better than 90% of the people using it, periodt 💅

and for the cute lil' sign-off: the footer of this page is just the page tag itself, VMATCH(1) — no date stamp, no source line drama, just the name chillin' at the bottom like main character energy 👑 so nothing extra to report there, bestie, that's fr fr the whole thing 🌸

go touch some grass and then come back and grep something, mwah 💜✨