ProtMap

Input
Target sequence   Place your query file with nucleotide sequences in FASTA format
Query sequence(s)   Place your second file with 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.
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
Alignment accurancy  Alignment accurancy:
Weak (fast)
Normal (slow)
Mapping accurancy  Mapping accurancy:
Weak (fast)
Normal (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.
Produce different variants of alignments Produce given different variants of alignments. "All" - all possible variants
Produce alternate variants of alignments Produce given best alternate variants of alignments. Value "All" - all possible variants
Produce best non-overlapped alignments 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).
Use consensus only for target sequenceIf target sequence is per-aligned profile then during alignment process will be used target sequence consensus instead profile
Use consensus only for query sequenceIf query sequence is per-aligned profile then during alignment process will be used query sequence consensus instead profile
Don't check mapping result for validityDon't check mapping result for validity
Maximal allowed intron lengthMaximal allowed intron length