EPRIMER3(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 EPRIMER3(1e) 💖

okay bestie, so this is a page from the EMBOSS Manual for Debian, and the star of the show is eprimer3 — she picks PCR primers and hybridization oligos and she is so good at it. 🧬✨

✨ NAME ✨

eprimer3 — Picks PCR primers and hybridization oligos 🎀

🌸 SYNOPSIS 🌸

eprimer3 -sequence seqall [-primer toggle] -task list
         [-hybridprobe toggle] -mishyblibraryfile infile
         -mispriminglibraryfile infile [-numreturn integer]
         [-includedregion range] [-targetregion range]
         [-excludedregion range] [-forwardinput string]
         [-reverseinput string] -gcclamp integer -osize integer
         -minsize integer -maxsize integer -otm float -mintm float
         -maxtm float -maxdifftm float -ogcpercent float -mingc float
         -maxgc float -saltconc float -dnaconc float -maxpolyx integer
         -psizeopt integer -prange range -ptmopt float -ptmmin float
         -ptmmax float -oexcludedregion range -oligoinput string
         -osizeopt integer -ominsize integer -omaxsize integer
         -otmopt float -otmmin float -otmmax float -ogcopt float
         -ogcmin float -ogcmax float -osaltconc float -odnaconc float
         -oanyself float -oendself float -opolyxmax integer
         -omishybmax float -explainflag boolean -fileflag boolean
         -firstbaseindex integer -pickanyway boolean
         -maxmispriming float -pairmaxmispriming float
         -numnsaccepted integer -selfany float -selfend float
         -maxendstability float -outfile outfile

eprimer3 -help

🦋 DESCRIPTION 🦋

eprimer3 is a command line program from EMBOSS — that's “the European Molecular Biology Open Software Suite” 💫. She's part of the "Nucleic:Primers" command group(s), and she's literally the moment. 👑

💅 OPTIONS 💅

🍓 Input section 🍓

-sequence seqall — The sequence from which to choose primers. The sequence must be presented 5' to 3'.
-primer toggle — Tell EPrimer3 to pick primer(s). Default value: Y.
-task list — Tell EPrimer3 what task to perform. Legal values are 1: 'Pick PCR primers', 2: 'Pick forward primer only', 3: 'Pick reverse primer only', 4: 'No primers needed'. Default value: 1.
-hybridprobe toggle — An 'internal oligo' is intended to be used as a hybridization probe (hyb probe) to detect the PCR product after amplification. Default value: N.
-mishyblibraryfile infile — Basically the same energy as MISPRIMING-LIBRARY, except the thing we're trying to dodge is hybridization of the internal oligo to sequences in this library instead of priming from them. The file must be in (a slightly restricted) FASTA format (W. B. Pearson and D.J. Lipman, PNAS 85:8 pp 2444-2448 [1988]); we briefly discuss the organization of this file below. If this parameter is specified then EPrimer3 locally aligns each candidate oligo against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds INTERNAL-OLIGO-MAX-MISHYB. (The maximum value of the weight is arbitrarily set to 12.0.) Each sequence entry in the FASTA-format file must begin with an 'id line' that starts with '>'. The contents of the id line is 'slightly restricted' in that EPrimer3 parses everything after any optional asterisk ('*') as a floating point number to use as the weight mentioned above. If the id line contains no asterisk then the weight defaults to 1.0. The alignment scoring system used is the same as for calculating complementarity among oligos (e.g. SELF-ANY). The remainder of an entry contains the sequence as lines following the id line up until a line starting with '>' or the end of the file. Whitespace and newlines are ignored. Characters 'A', 'T', 'G', 'C', 'a', 't', 'g', 'c' are retained and any other character is converted to 'N' (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to 'N'). There are no restrictions on line length. An empty value for this parameter indicates that no library should be used.
-mispriminglibraryfile infile — The name of a file containing a nucleotide sequence library of sequences to avoid amplifying (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified.) The file must be in (a slightly restricted) FASTA format (W. B. Pearson and D.J. Lipman, PNAS 85:8 pp 2444-2448 [1988]); we briefly discuss the organization of this file below. If this parameter is specified then EPrimer3 locally aligns each candidate primer against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds MAX-MISPRIMING. (The maximum value of the weight is arbitrarily set to 100.0.) Each sequence entry in the FASTA-format file must begin with an 'id line' that starts with '>'. The contents of the id line is 'slightly restricted' in that EPrimer3 parses everything after any optional asterisk ('*') as a floating point number to use as the weight mentioned above. If the id line contains no asterisk then the weight defaults to 1.0. The alignment scoring system used is the same as for calculating complementarity among oligos (e.g. SELF-ANY). The remainder of an entry contains the sequence as lines following the id line up until a line starting with '>' or the end of the file. Whitespace and newlines are ignored. Characters 'A', 'T', 'G', 'C', 'a', 't', 'g', 'c' are retained and any other character is converted to 'N' (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to 'N'). There are no restrictions on line length. An empty value for this parameter indicates that no repeat library should be used.

🌈 Additional section 🌈

(no cap, this section is just vibing here empty — nothing in it yet 🫶)

👑 Program options 👑

-numreturn integer — The maximum number of primer pairs to return. Primer pairs returned are sorted by their 'quality', in other words by the value of the objective function (where a lower number indicates a better primer pair). Caution: setting this parameter to a large value will increase running time. Default value: 5.

🧚 Sequence options 🧚

-includedregion range — A sub-region of the given sequence in which to pick primers. For example, often the first dozen or so bases of a sequence are vector, and should be excluded from consideration. The value for this parameter has the form (start),(end) where (start) is the index of the first base to consider, and (end) is the last in the primer-picking region.
-targetregion range — If one or more Targets is specified then a legal primer pair must flank at least one of them. A Target might be a simple sequence repeat site (for example a CA repeat) or a single-base-pair polymorphism. The value should be a space-separated list of (start),(end) pairs where (start) is the index of the first base of a Target, and (end) is the last E.g. 50,51 requires primers to surround the 2 bases at positions 50 and 51.
-excludedregion range — Primer oligos may not overlap any region specified in this tag. The associated value must be a space-separated list of (start),(end) pairs where (start) is the index of the first base of the excluded region, and and (end) is the last. This tag is useful for tasks such as excluding regions of low sequence quality or for excluding regions containing repetitive elements such as ALUs or LINEs. E.g. 401,407 68,70 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68.
-forwardinput string — The sequence of a forward primer to check and around which to design reverse primers and optional internal oligos. Must be a substring of SEQUENCE.
-reverseinput string — The sequence of a reverse primer to check and around which to design forward primers and optional internal oligos. Must be a substring of the reverse strand of SEQUENCE.

💜 Primer options 💜

-gcclamp integer — Require the specified number of consecutive Gs and Cs at the 3' end of both the forward and reverse primer. (This parameter has no effect on the internal oligo if one is requested.)
-osize integer — Optimum length (in bases) of a primer oligo. EPrimer3 will attempt to pick primers close to this length. Default value: 20.
-minsize integer — Minimum acceptable length of a primer. Must be greater than 0 and less than or equal to MAX-SIZE. Default value: 18.
-maxsize integer — Maximum acceptable length (in bases) of a primer. Currently this parameter cannot be larger than 35. This limit is governed by the maximum oligo size for which EPrimer3's melting-temperature is valid. Default value: 27.
-otm float — Optimum melting temperature(Celsius) for a primer oligo. EPrimer3 will try to pick primers with melting temperatures are close to this temperature. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409-6412 and Breslauer, Frank, Bloecker and Marky, Proc. Natl. Acad. Sci. USA, vol 83, pp 3746-3750. Please refer to the former paper for background discussion. Default value: 60.0.
-mintm float — Minimum acceptable melting temperature(Celsius) for a primer oligo. Default value: 57.0.
-maxtm float — Maximum acceptable melting temperature(Celsius) for a primer oligo. Default value: 63.0.
-maxdifftm float — Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers. Default value: 100.0.
-ogcpercent float — Primer optimum GC percent. Default value: 50.0.
-mingc float — Minimum allowable percentage of Gs and Cs in any primer. Default value: 20.0.
-maxgc float — Maximum allowable percentage of Gs and Cs in any primer generated by Primer. Default value: 80.0.
-saltconc float — The millimolar concentration of salt (usually KCl) in the PCR. EPrimer3 uses this argument to calculate oligo melting temperatures. Default value: 50.0.
-dnaconc float — how many nanomoles per liter of annealing oligos are floating around in your PCR 🧪. EPrimer3 uses this to do the oligo melting-temp math. The default (50nM) is lowkey perfect for the standard protocol they use over at the Whitehead/MIT Center for Genome Research — and bestie, that protocol is specific: 0.5 microliters of 20 micromolar concentration for each primer oligo in a 20 microliter reaction with 10 nanograms template, 0.025 units/microliter Taq polymerase in 0.1 mM each dNTP, 1.5mM MgCl2, 50mM KCl, 10mM Tris-HCL (pH 9.3) using 35 cycles with an annealing temperature of 56 degrees Celsius. This parameter is the 'c' in Rychlik, Spencer and Rhoads' equation (ii) (Nucleic Acids Research, vol 18, num 21), where a suitable value (for a lower initial concentration of template) is 'empirically determined'. Also, heads up: this value is less than the actual concentration of oligos in the reaction, because it's the concentration of annealing oligos, which depends on how much template (including PCR product) is hanging out in a given cycle. That concentration goes way up during a PCR — but fortunately PCR seems quite robust for a variety of oligo melting temperatures, so it's fine 💅. See ADVICE FOR PICKING PRIMERS. Default value: 50.0
-maxpolyx integer — the maximum allowable length of a mononucleotide repeat in a primer, like AAAAAA (no more stuttering, babe). Default value: 5

🌸 Product options 🌸

-psizeopt integer — the optimum size for the PCR product. 0 means there is no optimum product size, live your truth. Default value: 200
-prange range — these values say how long you want your product to be, as a space separated list of elements of the form (x)-(y) where an (x)-(y) pair is a legal range of lengths for the product. So if you want PCR products between 100 to 150 bases (inclusive) you'd set this parameter to 100-150. If you want products either in the range from 100 to 150 bases or in the range from 200 to 250 bases, set it to 100-150 200-250. EPrimer3 favors ranges to the left side of the parameter string, bestie — it will return legal primer pairs in the first range regardless of the value of the objective function for those pairs. Only if there aren't enough primers in the first range will EPrimer3 move on and return primers in a subsequent range. Default value: 100-300
-ptmopt float — the optimum melting temperature for the PCR product. 0 means there is no optimum temperature. Default value: 0.0
-ptmmin float — the minimum allowed melting temperature of the amplicon. Pls see the documentation on the maximum melting temperature of the product for details. Default value: -1000000.0
-ptmmax float — the maximum allowed melting temperature of the amplicon. Product Tm is calculated using the formula from Bolton and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11.46 (1989, CSHL Press):

Tm = 81.5 + 16.6(log10([Na+])) + .41*(%GC) - 600/length

Where [Na+} is the molar sodium concentration, (%GC) is the percent of Gs and Cs in the sequence, and length is the length of the sequence. A similar formula is used by the prime primer selection program in GCG, which instead uses 675.0/length in the last term (after F. Baldino, Jr, M.-F. Chesselet, and M.E. Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and formamide terms). The formulas here and in Baldino et al. assume Na+ rather than K+. According to J.G. Wetmur, Critical Reviews in BioChem. and Mol. Bio. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to .2 M Na+. EPrimer3 uses the same salt concentration value for calculating both the primer melting temperature and the oligo melting temperature. If you're planning to use the PCR product for hybridization later, this behavior will not give you the Tm under hybridization conditions 😭. Default value: 1000000.0

🧚 Internal oligo input 🧚

-oexcludedregion range — middle oligos may not overlap any region specified by this tag. The value must be a space-separated list of (start),(end) pairs, where (start) is the index of the first base of an excluded region, and (end) is the last. Often one would make Target regions excluded regions for internal oligos. Not me making boundaries so nobody crosses them 🚧
-oligoinput string — the sequence of an internal oligo to check and around which to design forward and reverse primers. Must be a substring of SEQUENCE. Periodt.

💖 Internal oligo options 💖

-osizeopt integer — optimum length (in bases) of an internal oligo. EPrimer3 will attempt to pick primers close to this length. Default value: 20
-ominsize integer — minimum acceptable length of an internal oligo. Must be greater than 0 and less than or equal to INTERNAL-OLIGO-MAX-SIZE. Default value: 18
-omaxsize integer — maximum acceptable length (in bases) of an internal oligo. Currently this parameter cannot be larger than 35 — that limit is governed by the maximum oligo size for which EPrimer3's melting-temperature is valid. Default value: 27
-otmopt float — optimum melting temperature (Celsius) for an internal oligo. EPrimer3 will try to pick oligos with melting temperatures that are close to this temperature. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409-6412 and Breslauer, Frank, Bloecker and Marky, Proc. Natl. Acad. Sci. USA, vol 83, pp 3746-3750. Pls refer to the former paper for background discussion. Default value: 60.0
-otmmin float — minimum acceptable melting temperature (Celsius) for an internal oligo. Default value: 57.0
-otmmax float — maximum acceptable melting temperature (Celsius) for an internal oligo. Default value: 63.0
-ogcopt float — internal oligo optimum GC percent. Default value: 50.0
-ogcmin float — minimum allowable percentage of Gs and Cs in an internal oligo. Default value: 20.0
-ogcmax float — maximum allowable percentage of Gs and Cs in any internal oligo generated by Primer. Default value: 80.0
-osaltconc float — the millimolar concentration of salt (usually KCl) in the hybridization. EPrimer3 uses this argument to calculate internal oligo melting temperatures. Default value: 50.0
-odnaconc float — the nanomolar concentration of annealing internal oligo in the hybridization. Default value: 50.0
-oanyself float — the maximum allowable local alignment score when testing an internal oligo for (local) self-complementarity. Local self-complementarity is taken to predict the tendency of oligos to anneal to themselves. The scoring system gives 1.00 for complementary bases, -0.25 for a match of any base (or N) with an N, -1.00 for a mismatch, and -2.00 for a gap. Only single-base-pair gaps are allowed. For example, the alignment 5' ATCGNA 3' || | | 3' TA-CGT 5' is allowed (and yields a score of 1.75), but the alignment 5' ATCCGNA 3' || | | 3' TA--CGT 5' is not considered. Scores are non-negative, and a score of 0.00 indicates that there is no reasonable local alignment between two oligos. Default value: 12.00
-oendself float — the maximum allowable 3'-anchored global alignment score when testing a single oligo for self-complementarity. The scoring system is as for the Maximum Complementarity argument. In the examples above the scores are 7.00 and 6.00 respectively. Scores are non-negative, and a score of 0.00 indicates that there is no reasonable 3'-anchored global alignment between two oligos. In order to estimate 3'-anchored global alignments for candidate oligos, Primer assumes that the sequence from which to choose oligos is presented 5' to 3'. INTERNAL-OLIGO-SELF-END is meaningless when applied to internal oligos used for hybridization-based detection, since primer-dimer will not occur. We recommend that INTERNAL-OLIGO-SELF-END be set at least as high as INTERNAL-OLIGO-SELF-ANY. Default value: 12.00
-opolyxmax integer — the maximum allowable length of an internal oligo mononucleotide repeat, for example AAAAAA. Default value: 5
-omishybmax float — similar to MAX-MISPRIMING except that this parameter applies to the similarity of candidate internal oligos to the library specified in INTERNAL-OLIGO-MISHYB-LIBRARY. Default value: 12.0

✨ Advanced section ✨

-explainflag boolean — if this flag is true, produce LEFT-EXPLAIN, RIGHT-EXPLAIN, and INTERNAL-OLIGO-EXPLAIN output tags, which are intended to provide information on the number of oligos and primer pairs that EPrimer3 examined, and statistics on the number discarded for various reasons. Default value: N
-fileflag boolean — if the associated value is true, then EPrimer3 creates two output files for each input SEQUENCE. File (sequence-id).for lists all acceptable forward primers for (sequence-id), and (sequence-id).rev lists all acceptable reverse primers for (sequence-id), where (sequence-id) is the value of the SEQUENCE-ID tag (which must be supplied). In addition, if the input tag TASK is 1 or 4, EPrimer3 produces a file (sequence-id).int, which lists all acceptable internal oligos. Default value: N
-firstbaseindex integer — this parameter is the index of the first base in the input sequence. For input and output using 1-based indexing (such as that used in GenBank and to which many users are accustomed) set this parameter to 1. For input and output using 0-based indexing set this parameter to 0. (This parameter also affects the indexes in the contents of the files produced when the primer file flag is set.) Default value: 1
-pickanyway boolean — if true, pick a primer pair even if LEFT-INPUT, RIGHT-INPUT, or INTERNAL-OLIGO-INPUT violates specific constraints. Default value: N
-maxmispriming float — the maximum allowed weighted similarity with any sequence in MISPRIMING-LIBRARY. Default value: 12.00
-pairmaxmispriming float — the maximum allowed sum of weighted similarities of a primer pair (one similarity for each primer) with any single sequence in MISPRIMING-LIBRARY. Default value: 24.00
-numnsaccepted integer — Maximum number of unknown bases (N) allowable in any primer.
-selfany float — the max allowable local alignment score when you're testing one single primer for (local) self-complementarity, AND the max allowable local alignment score when you're testing complementarity between the forward and reverse primers. Local self-complementarity is what we use to predict how much your primers wanna ~anneal to each other~ without necessarily causing self-priming in the PCR. Here's the scoring system bestie, write it down: 1.00 for complementary bases, -0.25 for a match of any base (or N) with an N, -1.00 for a mismatch, and -2.00 for a gap. Only single-base-pair gaps are allowed. So like, this alignment:

5' ATCGNA 3'
   ...|| | |
3' TA-CGT 5'

is allowed (and it yields a score of 1.75) 🎀 but this one:

5' ATCCGNA 3'
   ...|| | |
3' TA--CGT 5'

is not considered, sorry babe. Scores are non-negative, and a score of 0.00 means there is literally no reasonable local alignment between the two oligos. Default value: 8.00 ✨

-selfend float — the max allowable 3'-anchored global alignment score when testing a single primer for self-complementarity, and the max allowable 3'-anchored global alignment score when testing complementarity between forward and reverse primers. This 3'-anchored global alignment score is what predicts the likelihood of PCR-priming primer-dimers, like for example:

5' ATGCCCTAGCTTCCGGATG 3'
   .............||| |||||
3' AAGTCCTACATTTAGCCTAGT 5'

5' AGGCTATGGGCCTCGCGA 3'
   ...............||||||
3' AGCGCTCCGGGTATCGGA 5'

The scoring system is exactly like the Maximum Complementarity argument. In the examples above the scores are 7.00 and 6.00 respectively 👑 Scores are non-negative, and a score of 0.00 means there is no reasonable 3'-anchored global alignment between two oligos. So that you can estimate 3'-anchored global alignments for candidate primers and primer pairs, Primer assumes that the sequence you're choosing primers from is presented 5' to 3'. And heads up: it is nonsensical to give a larger value for this parameter than for the Maximum (local) Complementarity parameter, because the score of a local alignment will always be at least as great as the score of a global alignment. Like, math said no 💀 Default value: 3.00

💅 Primer penalty weights 💅

-maxendstability float — the maximum stability for the five 3' bases of a forward or reverse primer. Bigger numbers mean more stable 3' ends. The value is the maximum delta G for duplex disruption for the five 3' bases, as calculated using the nearest neighbor parameters published in Breslauer, Frank, Bloecker and Marky, Proc. Natl. Acad. Sci. USA, vol 83, pp 3746-3750. EPrimer3 uses a completely permissive default value for backward compatibility (which they may change in the next release, so watch this space 👀). Rychlik recommends a maximum value of 9 (Wojciech Rychlik, 'Selection of Primers for Polymerase Chain Reaction' in BA White, Ed., 'Methods in Molecular Biology, Vol. 15: PCR Protocols: Current Methods and Applications', 1993, pp 31-40, Humana Press, Totowa NJ). Default value: 9.0 🦋

🌸 Output section 🌸

-outfile outfile — that's it. That's the whole entry. The page does not give a description for this one, bestie, so we're not gonna invent one 🙈 (iykyk, output goes in the outfile.)

😭 BUGS 😭

Found a bug? Not the vibe, but okay. Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). Go off, tell them everything 🫶

✨ SEE ALSO ✨

eprimer3 is fully documented via the tfm(1) system. periodt 💅

👑 AUTHOR 👑

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

Wrote the script used to autogenerate this manual page. iconic behaviour fr fr 🌈

💖 COPYRIGHT 💖

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. 🎀

okay and that's the whole page bestie!! 💜 the footer says EMBOSS 6.4.0, dated 05/11/2012, and it's the manual for EPRIMER3(1e). you're so welcome, go design some primers, slay 🧚💅✨

📦 where this page comes from

debian bookworm: emboss 6.6.0+dfsg-12 · emboss
debian trixie: emboss 6.6.0+dfsg-15 · emboss
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ubuntu noble: emboss 6.6.0+dfsg-12ubuntu2 · emboss
ubuntu questing: emboss 6.6.0+dfsg-15ubuntu2
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ubuntu stonking: emboss 6.6.0+dfsg-19 · emboss
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