SeqMatch-P

Input
Target sequence   Place your query file with protein sequences in FASTA format.
Query sequence(s)   Place input file with one ore more protein sequences in FASTA format.
Output
Result   Name of the output file.
FormatOutput 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 methodScoring 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.
Fine adjustment   Fine adjustment of alignment blocks ends.
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
Different variants Produce given different variants of alignments. "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.
Translation table   Select translation table (Bacterial is default).