Sequences - peptide, DNA, RNA

Peptide sequence format

Code: peptide

Peptides can be entered using one or three letter amino acid abbreviations.

A text file containing sequences should contain only one type of sequence (only one or only three lettered sequences but not both). Each line must have one and only one continuous line in the text file without spaces. Abbreviations used:

3-letter	Ala	Arg	Asn	Asp	Asx	Cys	Gln	Glu	Glx	Gly	His	Ile	Leu	Lys	Met	Phe	Pro	Pyl	Sec	Ser	Thr	Trp	Tyr
1-letter	A	R	N	D	B	C	Q	E	Z	G	H	I	L	K	M	F	P	O	U	S	T	W	Y

Example

Valid files

PPPALPPKKR
APTMLPPASDFA

ProProProAlaLeuProProLysLysArg
AlaProThrMetProProProLeuProPro

Invalid files

PPPALPPKKR
AlaProThrMetProProProLeuProPro

ProProProAlaLeuProProLysLysArg
AlaProThrMetPPPLPP

Custom amino acids

In addition to the amino acids listed above, custom amino acids dictionary can be defined.

The custom_aminoacids.dict file is stored in the .chemaxon directory (UNIX) or the user's chemaxon directory using MS Windows.

The usual format of the dictionary file is:

molName=L-Alanine    Ala    A    [#6;A;H3X4][#6@H;H1X4]([#7;A;X3])-[#6]=O |wD:1.1,(3.85,-1.33,;2.31,-1.33,;1.54,-2.67,;1.54,,;)|    3    4
molName=L-Cysteine    Cys    C    [#7;A;X3][#6@@H;H1](-[#6H2]-[#16H1])-[#6]=O |wD:1.0,(1.54,-2.67,;2.31,-1.33,;3.85,-1.33,;4.62,-2.67,;1.54,,;)|    1    5    4

where the corresponding columns are:

field	description
name	optional (introduced in Marvin 6.2) molName=name
long (three-letters code) abbreviation	A capital letter followed by two small onesAla
short (one-letter code) abbreviation	X followed by characters in parentheses. Allowed characters are the letters of the alphabet, numbers and the dash character, e.g. molName=Sarcosine Sar X(Sar) ....
SMARTS representation of the amino acid fragment without terminal OH	Note the SMARTS strings representing amino acid fragments are denoting the hydrogens and sometimes the connection numbers to avoid ambiguity.For example if only the C[C@H](N)C=O string is used for L-alanine in the first example, this would match for many other amino acids as well as some of them are "containing" this string as a substructure. No query bonds allowed.
coordinates of the structure	Molecular coordinates are needed for cleaning. If they are missing, Ctrl+2 creates the coordinates for the structure.Coordinates can be generated by Molconvert using: cxsmarts:c option
the number of the backbone nitrogen in the SMARTS string	3 for Ala in the first example
the number of the C terminal carbon	4 for Ala in the first example
the number for other attachment point if needed	4 for L-cysteine in the second example

The columns should be separated by Tab characters.

The name is an optional field. If omitted, the entry should start directly with the 3-letter abbreviation (no Tab character is required).

Example

Phosphoserine can be added as a custom amino acid to the dictionary as follows:

molName=Phosphoserine   Sep     X(Sep)  [#7]-[#6@@H](-[#6]-[#8]P([#8])([#8])=O)-[#6]=O |(1.54,-2.67,;2.31,-1.33,;3.85,-1.33,;4.62,-2.67,;6.16,-2.67,;7.7,-2.67,;6.16,-1.13,;6.16,-4.21,;1.54,,;)|       1       9

To describe an aromatic custom amino acid both the aromatic and the Kekule form should be in the custom_aminoacids.dict file with the same short and long names.

See also
Peptide import and export options

DNA/RNA sequence format

DNA/RNA sequences can be entered using one letter nucleic acid abbreviations. Each line must have one and only one continuous line in the text file without spaces. Abbreviations used:

DNA	A	C	G	T
RNA	A	C	G	U

Code : dna, rna

Example

Valid files:

ACGTACGT
ACCCCGTGGGT

A-C-G-T-A-C-G-T
A-C-C-C-C-G-T-G-G-G-T

dA-dC-dG-dT-dA-dC-dG-dT
dA-dC-dC-dC-dC-dG-dT-dG-dG-dG-dT

Invalid files

acgtacgt