Chain alignments

The chain_alignments module is designed for the sequence comparsion by chaining alignment hits from self-sequence alignment.

Input data:

The chain_alignments alignment module expects alignment hits coordinate data between two distinct sequences, for example, from SegMantX’s generate_alignments module:

Click here to visit an example file containing alignments hits coordinate data

The input data for chain_alignments should be supplied in this format as tab-delimited file. Alternatively, a BLAST output format 7 file can be used, for example:

Click here to visit an example file containing a blast output format 7

Minimal example:

Chaining local alignments of a sequence alignment example towards sequence comparison:

SegMantX chain_alignments --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.alignment_coordinates.tsv -o tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv

• -i or --input_file: Input file received from ‘generate_alignments’ (i.e., five columns: q.start, q.end, s.start, s.end, identity). Alternatively, provide BLAST output format 7 and use –blast_outfmt7 flag).
• -o, --output_file: Filename of the chaining output file (Default: chaining_output.tsv).

Output:

Output of sequence alignment chaining module:

Click here to visit an example table for ‘chaining_output.tsv’

Click here to visit an example table for ‘chaining_output.tsv.indices’

Further options & parameters:

Using BLAST output format 7

To use a file derived from BLAST in output format 7 as input you can use the following flag:

• -B or --blast_outfmt7: Indicates if the input file is BLAST output format 7 (Default: False).

Example:

SegMantX chain_alignments --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.blast.x7 -o tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv --blast_outfmt7

Maximum gap size

To set a threshold for the max. gap size (in nucleotides) between alignment hits for chaining:

• -G or --max_gap: Maximum gap size between alignment hits for chaining (default: 5000).

To set the maximum gap size to 6000 (in nucleotides):

SegMantX chain_alignments --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.alignment_coordinates.tsv -o tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv --max_gap 6000

Scaled gap size

To set a threshold for the scaled gap size between alignment hits for chaining:

• SG or --scaled_gap: Minimum scaled gap between alignment hits for chaining (Default: 1.0).

To set the scaled gap to 2:

SegMantX chain_alignments --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.alignment_coordinates.tsv -o tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv --scaled_gap 2

Sequence topology of query

Choosing the correct sequence topology ensures that alignment hits on circular sequences (e.g., most plasmids or viral genomes) are correctly chained, even when fragmented due to their linear representation in FASTA-files. This is important for avoiding discontinuous alignments that can occur when aligning circular sequences in a linear format (i.e., FASTA format). The sequence topology is set to linear by default.

The sequence topology for the chaining can be set to circular using:

• -Q or --is_query_circular: Indicates a circular sequence topology of query (Default: False).
• -S or --is_subject_circular: Indicates a circular sequence topology of subject (Default: False).

Note, that on circular sequence topologies it is necessary to supply the sequence length to SegMantX (e.g., –sequence_length_query, –sequence_length_subject or –fasta_file_query, –fasta_file_subject). See below to see options how to provide the sequence length to SegMantX.

To set a circular sequence topology for query & subject:

SegMantX chain_alignments --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.alignment_coordinates.tsv -o tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv --is_query_circular --is_subject_circular --fasta_file_query tests/NZ_CP018634.1.fasta --fasta_file_subject tests/NZ_CP022004.1.fasta

Sequence length

The sequence length is required for correct alignment chaining on sequences with circular sequence topology.

To set the sequence length manually:

• -LQ, --sequence_length_query: Size of the query sequence (is required with circular sequence topology). Otherwise, provide fasta file (i.e., using –fasta_file_query) (Default: None).
• -LS, --sequence_length_subject: Size of the subject sequence (is required with circular sequence topology). Otherwise, provide fasta file (i.e., using –fasta_file_subject) (Default: None).

To set the sequence length manually for query and subject sequence:

SegMantX chain_alignments --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.alignment_coordinates.tsv -o tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv --is_query_circular --is_subject_circular --sequence_length_query 92831 --sequence_length_subject 59371

To determine the sequence length automatically from FASTA-file:

• -fq, --fasta_file_query: Fasta file to read out the sequence length. Required if the sequence topology is circular and –sequence_length_query is not provided manually.
• -fs, --fasta_file_subject: Fasta file to read out the sequence length. Required if the sequence topology is circular and –sequence_length_subject is not provided manually.

To set the sequence length automatically for the query and subject sequences by providing the FASTA-files:

SegMantX chain_alignments --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.alignment_coordinates.tsv --fasta_file_query tests/NZ_CP018634.1.fasta --fasta_file_subject tests/NZ_CP022004.1.fasta --is_query_circular --is_subject_circular -o tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv

Minimum alignment hit length

To discard alignment hits for chaining according to their length:

• -ml or --min_length: Minium length of alignment hits for chaining (default: 200).

To set the minimum alignment hit length to 300:

SegMantX chain_alignments --input_file tests/NZ_CP018634.1_vs_NZ_CP022004.1.alignment_coordinates.tsv -o tests/NZ_CP018634.1_vs_NZ_CP022004.1.chains.tsv --min_length 300