Split block (if possible).
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Split block recursively (if possible).
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Fine adjustment of block bounds.
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Use consensus only for target sequence, if target sequence is profile.
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Use consensus only for query sequence, if query sequence is profile.
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Scoring methods for whole sequence. Score is: 1 – Maximum fragment score (default). 2 – All blocks score (default). 3 – Blast-like score.
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Do not consider L-plets the number of which exceed this mathematical expectation.
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Do not consider L-plets with low complexity (L-plets consist of poly tracts (AAAAA..., ATATATAT... etc.))
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Output N best alignment (mainly non overlapped).
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Output N best alternative alignment.
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Output N best non overlapped alignment.
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Output homology blocks only (not alignment)
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Use group of symbols. N group numbers.
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Alignment region on target sequence does not exсeed given length.
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Alignment region on query sequence does not exceed given length.
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Alignment region on target sequence does not exceed length of second sequence multiplied to N (N - is floating point number.
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Alignment region on query sequence does not exceed length of first sequence multiplied to N (N - is floating point number).
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Alignment region on second sequence does not exceed length of first sequence multiplied to N (N - is floating point number).
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Alignment region on target sequence does not exceed length of second sequence plus N.
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Alignment region on query sequence does not exceed length of first sequence plus N.
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Use translation table. Table values are: 1 - Standard. (Default). 2 - Vertebrate Mitochondrial. 3 - Yeast Mitochondrial.
4 - Mold Mitochondria, Protozoan Mitochondrial, Colenterate Mitochondrial, Mycoplasma, Spiroplasma.
5 - Invertebrate Mitochondrial. 6 - Ciliate Nuclear, Dasycladacean Nuclear, Hexamita Nuclear.
9 - Echinoderm Nuclear. 10 - Euplotid Nuclear. 11 - Bacterial. 12 - Alternative Yeast Nuclear.
13 - Ascidian Mitochondrial. 14 - Flatworm Mitochondrial. 15 - Blepharisma Macronuclear.
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Target sequence is prealigned profile.
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Query sequence is prealigned profile.
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Scan target sequence in different chain: 0 - In direct chain only (default). 1 - In reverse chain only. 2 - In both chains.
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Scan query sequence in different chain: 0 - In direct chain only (default). 1 - In reverse chain only. 2 - In both chains.
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Get target sequence from this position (default value 1).
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Get target sequence to this position (0 - get to end, default value 0.
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Get query sequence from this position (default value 1).
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Get query sequence to this position (0 - get sequences to end, default value 0).
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Options "Get target sequence from this position" and "Get target sequence to this position" are applied to complimentary chain of target sequence.
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Options "Get query sequence from this position" and "Get query sequence to this position" are applied to complimentary chain of query sequence.
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Remove trailing X symbols from target sequence.
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Remove trailing X symbols from query ( or base) sequence.
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Remove polyA tail from target sequence.
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Remove polyA tail from query (or base) sequence.
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Remove polyT head from target sequence.
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Remove polyT head from query (or base) sequence.
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Maximal length of readed name (default value 80), if = 0 full length.
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Assume target sequence is preliminary complemented.
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Assume query sequence is preliminary complemented.
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Global alignment with tail gaps by dynamic programming.
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Global alignment without tail gaps by dynamic programming.
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Local alignment by dynamic programming.
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To use step N on target sequence
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To use step N on query sequence.
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Use separator between lines of alignment.
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Print alignment for N symbols in each line (Default setting: 60).
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Do not output unaligned flanks outside alignment.
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Title type: 1 - title doesn't appear. 0 - the title appears as follows: [DR] Sequence: 2( 6), S: 122.41, L: 441 Sequence_Name; 2 - the title appears as follows: [DR] Sequence: 2( 6) S: 122.41 L: 4411 RL: 4411 AC: 919.0 Name:Sequence_Name; 3- the title appears as follows: [DR] Sequence: 2( 6), Name:Sequence_Name S: 122.41 L: 4411529 RL: 4411529 AC: 919.0
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Additionally print non translated sequence (when "Output mode"=2 or 3 specified).
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Print alignment for N symbols in flank of alignment block (Default setting: 15).
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This value will be added to target sequence numeration on output.
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This value will be added to query sequence numeration on output.
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Print progress information for each N processed base sequences.
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Print progress information for each N processed base sequences to stderr.
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Sort regions of homology by: 0 - No sorting (default). 1 - Location. 2 - Score.
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Output alignment in HTML format.
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N – html color value
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Output alignment result just at alignment process. Default value - on.
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Don’t print a header of result after sorting.
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Do not verify accuransy of first exon.
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No filters no splice site setting. Alignment as it is.
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Do not filter inconsistent alignment, but process each alignment.
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Use Some additional minor procedures for more precision.
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Do not consider GC donor site.
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Put here other options, if any. | |