BioSequenceModify

BioSequenceModify[seq,"mod"]

gives the result of applying the modification "mod" to the sequence seq.

BioSequenceModify[seq,{"mod",params}]

specifies the parameters params for "mod".

BioSequenceModify[modspec]

represents an operator form of BioSequenceModify that can be applied to a biomolecular sequence.

Details

  • Bond modifications:
  • {"AddBond",{i1,i2}}add a higher-order bond between letters at i1 and i2
    {"AddBond",Bond[{i1,i2},"type"]}add a bond of the given type between the given indices
    {"DeleteBond",{i1,i2}}remove all higher-order bonds between the given indices
    {"DeleteBond",Bond[{i1,i2},"type"]}remove the specified bond between the given indices
  • Circularity adjustment modifications:
  • "MakeCircular"convert a linear sequence into a circular sequence
    "MakeLinear"convert a circular sequence into a linear sequence
    {"MakeLinear",i}convert to a linear sequence, starting at the i^(th) position
  • Collection modifications:
  • {"AddToCollection",{seq1,seq2,…}}incorporate a list of sequences into a sequence collection
    "SplitDisconnectedCollection"separate unbonded clusters into separate collections
  • Representation-only modifications:
  • "InnermostBondRepresentation"represent bonds at the innermost applicable sequence
    "OutermostBondRepresentation"represent bonds at the outermost sequence
    "CanonicalRepresentation"convert all sequences and bonds to a canonical form
  • Translation modifications:
  • "DropIncompleteCodons"drop incomplete codons from the end of DNA or RNA
    "DropToStartCodon"drop letters from DNA or RNA until a start codon is found
    "DropFromStopLetter"drop the letters from a peptide after a stop letter is found

Examples

open allclose all

Basic Examples  (12)

Add a bond to a sequence:

Delete a bond from a sequence:

Represent all bonds at the innermost sequence, with all letters included:

Represent all bonds at the outermost sequence:

Canonicalize the representation of bonds and sequences into a sorted and reduced form:

Convert a linear sequence to a circular sequence:

Convert a circular sequence to a linear sequence:

Add a list of sequences into a sequence collection:

Separate the unbound components of a sequence collection into separate collections:

Drop letters at the end of a nucleotide sequence so only complete codons are present for translation:

Drop the letters up to a start codon in the default genetic translation table:

Drop terms after the stop letter in a peptide sequence:

Scope  (23)

"AddBond"  (4)

A bond type does not need to be specified to insert a bond. If one is not given, it will be inferred:

The type of the bond inferred may depend on the letters being linked:

Bonds can be added to hybrid strands:

Bonds can be added to sequence collections:

"AddToCollection"  (3)

A single sequence can also be added to a collection:

A single motif or hybrid sequence will be modified into a collection:

If there are multiple sequence collections, they will be merged in the result:

"CanonicalRepresentation"  (3)

If sequences are identical, canonicalization will use strand-level bonds for ordering:

If the sequences and strand-level bonds are identical, canonicalization will use sequence bonds for ordering:

In addition to sorting, single-strand collections are reduced to the strand and single motif hybrids are reduced to the motif:

"DeleteBond"  (2)

Delete all higher-order bonds between the two indexes:

Deleting bonds always works on the outermost form, which is the form given by the "SequenceBondList" property:

"DropToStartCodon"  (3)

Any genetic translation table entity can be used to specify start codons:

A specific codon or list of codons can be used as the start codon specification:

Modifications can be created in an operator form for later use:

Modifications with further specifications can also be used in operator form:

"InnermostBondRepresentation"  (1)

Moving bonds inward can potentially bring them into the motif from several layers:

"MakeCircular"  (2)

RNA sequences can be converted to circular RNA sequences:

Peptide sequences can be converted to circular peptide sequences:

"MakeLinear"  (3)

Circular RNA sequences can be converted to linear RNA sequences:

Circular peptide sequences can be converted to linear peptide sequences:

Start the linear sequence from a specific position:

Relative bond positions are preserved when converting circular sequences to linear sequences:

"OutermostBondRepresentation"  (1)

Moving bonds inward will bring them from inside any motif or strand to the outermost sequence structure:

"SplitDisconnectedCollection"  (1)

Splitting connections will renumber bonds based on new collection memberships:

Applications  (1)

A circular peptide:

Various peptides can be related to each other through a circular permutation:

Possible Issues  (2)

A given modification may not apply to a particular type of sequence:

If a bond type cannot be inferred, an untyped bond is added:

Neat Examples  (1)

Represent the protein preproinsulin as a BioSequence:

Remove the signal peptide sequence to make proinsulin:

Add the disulfide bonds and split the proinsulin sequence to make insulin:

Wolfram Research (2020), BioSequenceModify, Wolfram Language function, https://reference.wolfram.com/language/ref/BioSequenceModify.html (updated 2021).

Text

Wolfram Research (2020), BioSequenceModify, Wolfram Language function, https://reference.wolfram.com/language/ref/BioSequenceModify.html (updated 2021).

CMS

Wolfram Language. 2020. "BioSequenceModify." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2021. https://reference.wolfram.com/language/ref/BioSequenceModify.html.

APA

Wolfram Language. (2020). BioSequenceModify. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/BioSequenceModify.html

BibTeX

@misc{reference.wolfram_2023_biosequencemodify, author="Wolfram Research", title="{BioSequenceModify}", year="2021", howpublished="\url{https://reference.wolfram.com/language/ref/BioSequenceModify.html}", note=[Accessed: 03-December-2023 ]}

BibLaTeX

@online{reference.wolfram_2023_biosequencemodify, organization={Wolfram Research}, title={BioSequenceModify}, year={2021}, url={https://reference.wolfram.com/language/ref/BioSequenceModify.html}, note=[Accessed: 03-December-2023 ]}