Synopsis
Description
CStranslate translates a sequence or alignment into an abstract state alphabet (AS219). This tool is part of the CS-BLAST package and is used for context-specific sequence representation.Required Parameters
Input file with alignment or sequence
Output Options
Output file for generated abstract state sequence (default: <infile>.as)
Append generated abstract state sequence to this file
Output format:
seq: abstract state sequenceprf: abstract state profile
Input Options
Input format: prf, seq, fas, a2m, a3m, or ca3m (default: auto-detect from file extension)
Match column assignment for FASTA alignments:
-1(default): make columns with residue in first sequence match columns[0-100]: make all FASTA columns with less than X% gaps match columns
Pseudocount Options
Abstract state alphabet consisting of exactly 219 states
Add context-specific pseudocounts using given context-data
Pseudocount admix for context-specific pseudocounts (range: 0-1)
Constant in pseudocount calculation for alignments (range: 0-inf)
Weight of abstract state column in emission calculation (range: 0-inf)
FFindex Options
Enable FFindex mode: read from -i <ffindex>, write to -o <ffindex> (do not include _ca3m suffix for ca3m informat). Enables OpenMP if available.
Other Options
Verbose mode: show progress and results
Examples
Translate sequence to abstract states
Translate alignment with custom pseudocount parameters
Process FFindex database
Output Format
The tool produces abstract state sequences in AS219 alphabet, which represents protein sequences using 219 context-dependent states. When verbose mode is enabled, it shows:- Position numbers
- Consensus sequence
- Match symbols indicating confidence
- AS219 sequence
- Confidence values (0-9)
Exit Codes
0: Success1: Error reading input file2: Invalid parameters