Input | |
Target sequence | Place your query file with nucleotide sequences. |
Query sequence(s) | Place file with one ore more nucleotide sequences. |
Output | |
Result | Name of the output file. |
Format | Output format:
List of alignment blocks coordinates List of alignment blocks coordinates and blocks sequences Output alignment (default) General alignment information General alignment information, blocks list and alignment |
Sort blocks | Sort regions of homology for "List of alignment blocks coordinates" value of "Output format" option :
Don't sort (default) Incremental on Target Incremental on Query Decremental by score Decremental by weight Decremental by length |
Flank type | Flank type:
Length - Output for given amount of symbols in flank of alignment block. All - Unlimited flank |
Position number | Print additional strings with position number for target and query strings. |
Numeration Offset | Numeration Offset:
Target - Given value will be added to taget sequence numeration on output Query - Given value will be added to query sequence numeration on output |
Special symbols: | Special symbols:
Homology - Output symbol as separator lines between target and query, each line separator position shows similarity between target and query positions Gap - Use given simbol to print output gaps Tailing Gap - Use given simbol to print output flanking gaps in profile output, default: '-' Line Tearing - String used for displaying of big gaps in alignment. |
Output string | Output for given amount of symbols in each line. |
Unalignment info | Produce output information for sequences where no similarity found. |
Perfect only | Output perfect and near-perfect alignment. |
Preprocessing | |
Remove | Remove:
PolyA - Remove polyA tail from taget sequence. It is may be useful if target sequence is mRNA or EST. PolyT - Remove polyT head from taget sequence. It is may be useful if target sequence is complemented mRNA or EST. Trailing N - Remove trailing N symbols from both ends of target sequence. |
Cut Sequence | Cut Sequence:
Start - Search in target sequence from given position End - Search in target sequence to given position. "0" - get to end |
Apply to chain | Search in target sequence is applied to reverse chain. |
Options | |
Alignment accurancy | Alignment accurancy:
Weak (fast) Normal (slow) |
Mapping accurancy | Mapping accurancy:
Weak (fast) Normal (slow) |
Score method | Scoring methods for whole alignment:
No scoring the alignment (default) By probability of the best block in alignment By probability of the summary of all blocks Blast-like (in SD units) Blast-like (in probability units) |
Threshold | If alignment has score less then given value then alignment is not printed. |
Target chain(s) | Search in chain(s) in target:
In direct chain only In reverse chain only In both chains |
Fine adjustment | Fine adjustment of alignment blocks ends. |
Multiply variants: |
Alternate variants
- Produce given best alternate variants of alignments. "All" - Produce all alternate variants of alignments. "Number" - Produce given best alternate variants of alignments.
Non-overlapped variants - Produce given non-overlapped variants of alignments. "All" - Produce all alternate variants of alignments. "Number" - Produce given best non-overlapped alignments. Different variants - Produce given different variants of alignments. "All" - Produce all alternate variants of alignments. "Number" - Produce different variants of alignments. |
Local alignment | Produce local alignment. Split alignment to several local alignments. |
Split diagonal recursively | Split diagonal recursively (if possible). |
Restrictions | Target:
By length - Alignment region on target sequence does not exceed given length. By multiplier - Alignment region on target sequence does not exceed length of query sequence multiplied to N (N - is floting poin number). By range - Alignment region on target sequence does not exceed length of query sequence plus N. Query: By length - Alignment region on query sequence does not exceed given length. By multiplier - Alignment region on query sequence does not exceed length of query sequence multiplied to N (N - is floting poin number). By range - Alignment region on query sequence does not exceed length of query sequence plus N. |
Maximal allowed intron length | Maximal allowed intron length |