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SeqMatch-N |
| Input | |
| Target sequence | Place your query file with nucleotide sequences. |
| Query sequence(s) | Place file with one ore more nucleotide sequences. |
| Format |
Input file format:
Packed - Packed format Fasta - Fasta format |
| Output | |
| Result | Name of the output file. |
| Format | Output format:
List of alignment blocks coordinates (default) List of alignment blocks coordinates and blocks sequences Output alignment 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 sort by coordinates on target Incremental sort by coordinates on Query Decremental sort by alignment block score Decremental sort by alignment block weight Decremental sort by alignment block 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 |
| 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. |
| Graphic data | Name of the output binary t-file. |
| Preprocessing | |
| 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 | |
| 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 | |
| Precision | Precision:
Rough alignment (fast) Fast alignment (slow) |
| Score method | Scoring methods for whole alignment:
No scoring the alignment (default) Score of alignment is the probability of the best block in alignment Score of alignment is the probability of the summ of all blocks of alignment Blast-like scoring method (in SD units) Blast-like scoring method (in probability units) |
| Threshold | If alignment has score less then given value then alignment is not printed. |
| Search in chain(s) in target | 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. |
| Different variants | Produce given different variants of alignments. "All" - all possible variants |
| Alternate variants | Produce given best alternate variants of alignments. Value "All" - all possible variants |
| Non-overlapped variants | Produce given non-overlapped variants of alignments. Value "All" - all possible variants |
| Local alignment | Produce local alignment. Split alignment to several local alignments. |
| Split alignment block | This option allows to split alignment block to two blocks with better quolity |
| Split diagonal recursively | Split diagonal recursively (if possible). |
| Target | |
| By length | Alignment region on target sequence does not exeed given length. |
| By multiplier | Alignment region on target sequence does not exeed length of query sequence multiplied to N (N - is floting poin number). |
| By range | Alignment region on target sequence does not exeed length of query sequence plus N. |
| Query | |
| By length | Alignment region on query sequence does not exeed given length. |
| By multiplier | Alignment region on query sequence does not exeed length of query sequence multiplied to N (N - is floting poin number). |
| By range | Alignment region on query sequence does not exeed length of query sequence plus N. |