Skylign

POST /

URL:

http://sklign.org/

Parameters:

Name	Description
file required	A single file that will be converted into a logo. It should be either a profile HMM or a multiple sequence alignment in one of the following accepted formats: Aligned FASTA Clustal (and Clustal-like) PSI-BLAST PHYLIP Selex GCG/MSF STOCKHOLM format UC Santa Cruz A2M (alignment to model)
processing optional	The type of post processing to be performed on an alignment: observed - Letter stacks and gap values depend on estimated distributions for each position. Estimate those distributions directly from observed frequencies. weighted - Letter stacks and gap values depend on estimated distributions for each position. Redundant sequences are downweighted, and distributions are estimated from frequencies computed using those sequence weights. hmm - Letter stacks and gap values depend on estimated distributions for each position. Use HMMER to estimate those distributions by applying sequence weights, absolute weights, and a Dirichlet mixture prior. hmm_all - Default: observed
letter_height optional	Which height calculation algorithm should be used during logo generation. There are three different algorithms to choose from: info_content_all - Stack height of each position is that position's information content. All letters are shown, subdividing stack height according to estimated letter probability. info_content_above - Stack height of each position is that position's information content. Positive-scoring (above background frequency) letters are shown, subdividing stack height according to estimated letter probability. score - In each position, letter height is the score of that letter at that position. Only positive-scoring letters are shown. Stack height has no inherent meaning. Default: info_content_all

Name

Description

file
required

A single file that will be converted into a logo. It should be either a profile HMM or a multiple sequence alignment in one of the following accepted formats:

Aligned FASTA
Clustal (and Clustal-like)
PSI-BLAST
PHYLIP
Selex
GCG/MSF
STOCKHOLM format
UC Santa Cruz A2M (alignment to model)

processing
optional

The type of post processing to be performed on an alignment:

observed - Letter stacks and gap values depend on estimated distributions for each position. Estimate those distributions directly from observed frequencies.
weighted - Letter stacks and gap values depend on estimated distributions for each position. Redundant sequences are downweighted, and distributions are estimated from frequencies computed using those sequence weights.
hmm - Letter stacks and gap values depend on estimated distributions for each position. Use HMMER to estimate those distributions by applying sequence weights, absolute weights, and a Dirichlet mixture prior.
hmm_all -

Default: observed

letter_height
optional

Which height calculation algorithm should be used during logo generation. There are three different algorithms to choose from:

info_content_all - Stack height of each position is that position's information content. All letters are shown, subdividing stack height according to estimated letter probability.
info_content_above - Stack height of each position is that position's information content. Positive-scoring (above background frequency) letters are shown, subdividing stack height according to estimated letter probability.
score - In each position, letter height is the score of that letter at that position. Only positive-scoring letters are shown. Stack height has no inherent meaning.

Default: info_content_all

Repsonse Formats:

JSON, XML, YAML, Text, HTML

Example:

POST http://skylign.org/

# Request
curl -H 'Accept:application/json' -F file='@test.hmm' -F processing=hmm http://skylign.org/

# Response
{
  "url":"http://skylign.org/logo/6BBFEB96-E7E0-11E2-A243-DF86A4A34227",
  "uuid":"6BBFEB96-E7E0-11E2-A243-DF86A4A34227",
  "message":"Logo generated successfully"
}