AA-Annotator

Alignment Annotator

  cd /home/people/christo/public_html/strap/AA2/tmp/apache/x5a0ae26e54_13ad/; less -R stdout.txt

Author: christoph

gille

charite

de Institut für Biochemie, Charité, Berlin

DAS_features list of DAS services, list of proteins
Example:
- ```
    DAS_features CSA%20-%20extended uniprot cbs_total netphos netoglyc , UNIPROT:P29590
```
Position specific annotations are loaded from the DAS services and underlined in the alignment. Also see GFF_expasy_features

GFF file_or_GFF-line
Examples:

    GFF P25787	UniProtKB	Modified residue	24	24	.	.	.	Note=Phosphotyrosine

    GFF http://server/path/myGffFile.gff

Loads the GFF files and underlines the sequence features Also see DAS_features

GFF_expasy_features proteins
Example:
- ```
    GFF_expasy_features *
```
Loads the GFF files and underlines the sequence features Also see DAS_features and GFF
aa_sequence amino acid sequence , protein name
Example:
- ```
    aa_sequence -VLSAAERAQVKAAWGKI--QAGAHGAEALERMFLGFPTTKTYPF, Xenopus
```
Defines a protein by amino acid sequence. The sequence may have gaps "-".
accession_id id, protein
Example:
- ```
    accession_id UNIPROT:HSLV_ECOLI , hslv_ecoli
```
The accession ID for a protein is set. Providing the accession ID allows direct access to BioDAS services.
add_annotation selection_name, key, value
Example:
- ```
    add_annotation myProtein.pdb/myAnnotation1, Balloon, Another line
```
An entry consisting of a key such as "Remark" or "Balloon" and a value such as a free text is added to the named selection.
add_compound hetero-compound or nucleotide-chain , protein1 protein2
Example:
- ```
    add_compound  PDB:1gd2_A PDB:1gd2_B, 1gd2_E.pdb
```
Hetero-compounds or nucleotide chains are added. For HTML output only nucleotide chains of the same PDB id are regarded.
add_xref reference, protein
Example:
- ```
    add_xref PDB:1NED , hslv_ecoli
```
align proteins
Example:
- ```
    align *
```
Aligns the proteins
balloon_text Text , proteins and residue selections
Examples:
- ```
 balloon_text Example with html bold face. This is a greater than sign: &gt;, protein1
```
- ```
 balloon_text bla bla This is a greater than sign: >, protein1
```
- ```
 balloon_text NULL , protein1
```
Defines the mouse-over text for proteins and residue selections If certain html tags (lower case) are found in the text such as , or , then HTML is assumed. Only in this case certain characters need to be html encoded.
close protein1 protein2 ...
The proteins are removed from the view. The remain on the hard disk.
echo bla bla bla
Example:
- ```
    echo Hello world
```
The text is printed to standard output (console) or to a file specified with -scriptOutput=filePath
feature_colors name=color1,color2 name=color
Example:
- ```
    feature_colors Modified_residue=#FF2222,#FF0000 Phosphorylated_residue=#AAaa00 Glycosylated_residue=#00ffFF
```
Assignment of colors to sequence feature names. The first color is for black background and the other optional color is for white paper. All residue selections with one of those names will be treated as sequence features.
find_uniprot_id protein1 protein2 ...
The Uniprot identifier is important to query certain web resources. The uniprot entry which matches or contains the given sequence is determined.
hide proteins
The proteins are removed from the current alignment but remain in memory.

icon URL , protein
Examples:

    icon http://www.bioinformatics.org/strap/images/dog.png , protein

```
    icon NULL , protein
```

    icon data:image/gif;base64,R0lGODlhGgAaAIABADMzM////yH5BAEKAAEALAAAAAAaABoAAAI5jI+py+0Po0SgWmpry9nwq3yimIwmh51nqo5s+71wd8yuPIc2Xe7AZnvkIK3JauJBIVlLXfMJjUIKADs= , 4 5

The protein icon is displayed in the alignment row at the left.

load list of URLs or database IDs or file paths
The proteins are loaded
new_nucleotide_selection protein/selectionName, group, nucleotides
Similar to new_selection with the differenct that positions refer to the nucleotide sequence, the protein was translated from.
new_selection protein/selectionName, group, residues
Examples:
- ```
    new_selection   my_protein/N-terminus, group_test, 1-20
```
- ```
    new_selection   my_protein/a_selection, group_test, 10:-20: 30:
```
A residue selection for the given protein is created. The name of the selection is given after the slash. The group name allows to group selections that belong together. The residue subset can use the natural numbering starting at 1 or the PDB resn. The PDB resn is recognized by the colon according to the Rasmol convention.
open_3D ViewID, protein1 protein2 ...
The given proteins are opened in a 3D-viewer. ViewID is an identifier which allows this view to be refered to by the commands select_3D and close_3D.
print_3D_transformation proteins
Prints the 3x3 rotation matrix and translation vector of the given proteins.
print_proteins
Prints a list of all proteins to standard output (console) or to a file specified with -scriptOutput=filePath
print_residue_selections proteins
Prints a list of all residue selections of the proteins
project_coordinates PDB ID , protein
Examples:
- ```
    project_coordinates PDB:1BOR_A , UNIPROT:P29590
```
- ```
    project_coordinates AUTO , UNIPROT:P29590
```
- ```
    project_coordinates NULL , UNIPROT:P29590
```
The 3D coordinates are infered into the protein. With AUTO, the most similar PDB entry is determined automatically.
rotate_translate xx xy xz yx yy yz zx zy zz translation_x translation_y translation_z , protein
Examples:
- ```
    -0.51  -0.69   0.50   0.22   0.45   0.86  -0.82   0.55  -0.80     91.15 25.13  55.68 , protein
```
- ```
     NULL, protein
```
The protein is moved in 3D space. If a protein is given instead of a 3x3 matrix and translation vector then the transformation of that protein is used. Also see command "superimpose".
rotate_translate_protein_complex xx xy xz yx yy yz zx zy zz translation_x translation_y translation_z , protein
Works similar as rotate_translate. In addition, if protein is part of a multiprotein complex, then also all peptide chains of the complex are rotated and translated.

secondary_structure character-sequence , protein
Example:

    secondary_structure ---HHHHHH---HHHHH---EEEEEEEEEE----EEEEEE , Xenopus

select_3D 3D-ViewID, proteins or residue selections
Examples:
- ```
    select_3D  ViewID
```
- ```
    select_3D  ViewID , subtilisin
```
- ```
    select_3D  ViewID , subtilisin/100-200
```
Subsequent commands starting with "3D_" such as "3D_select" act on the selected 3D-view, protein (and residue selection). The first argument is the identifier of a 3D-view (See open_3D). The second argument is optional and is one or several proteins in this view or residue selections. Instead of referring to a particular view ID, the constant strings $ANY_VIEWER or $ANY_WIRE can be used. Note that the command "select_3D" and "3D_select" are different.
set_annotation selection_name, key, value
like add_annotation but already existing entries with this key are deleted.
set_characters_per_line number
Example:
- ```
    set_characters_per_line 60
```
Number of letters per line for non-interactive mode with command line export options -toHTML, -toClustal and -toMSF.
set_color hex color, proteins or residue selections
Examples:
- ```
    color #00FF00 , protein1
```
- ```
    color #00FF0066 , protein1
```
The color of residue selections or proteins can be changed. The color of the protein is used when a protein is loaded into the 3D view and rendered. If the color has 8 hexadecimal digits, the last two digits are the transparency.
set_color_mode color-type
Example:
- ```
    set_color_mode hydropathy
```
Residue colors. white|black|charge|hydropathy|chemical|nucleotide
set_conservation_threshold number
Example:
- ```
    set_conservation_threshold 70
```
Number is in the range of 0 to 100 and defines the threshold up from where conserved residues are emphasized.
set_nucleotide_index_offset number , protein
Change the numbering of residues A positive value shifts all nucleotide selections to the left
set_residue_index_offset number , protein
Change the numbering of residues
set_ruler_secondary_structure theProtein
The protein should have secondary structure information. A ruler is drawn above or below the alignment. Helices are red and beta sheets are yellow.
superimpose proteins
Example:
- ```
    superimpose *
```
Superimposes the proteins. The reference protein is the one that is most similar to all others
superimpose_protein_complexes protein1 protein2 ...
Multiprotein complexes as whole are superimposed upon each other. See define_protein_complex
translate_cds coding sequence expression , myProtein
Examples:
- ```
    cds join(10 20...30) , protein
```
- ```
    cds complement(join(10 20...30)) , myProtein
```
- ```
    cds 2 , myProtein
```
The protein myProtein is given as a genomic sequence. This command specifies, how the DNA is translated into protein. It takes a CDS expression (which is recognized by the dots) or a number or range of numbers which refer to the CDS expression[s] in the Embl or GB file.
use_aligner t_coffee
Set t_coffee as the default aligner. Possible arguments: clustalw, t_coffee, amap, clustalw, dialign, dialignt, kalign, mafft, muscle, probcons2
use_aligner3D mapsci
Set mapsci as the default aligner. Possible arguments: ce, mapsci, matt, mustang, native_ce, smolign, tm_align
use_aligner_p t_coffee
Set t_coffee as the default aligner allowing profiles. Possible arguments: clustalw, t_coffee

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