HomeAll softwareProductsNew ProductsServicesManagement teamCorporate ProfileContact

Test online

Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Next Generation
Gene search
Gene explorer
Promoter
Protein location
RNA structure
Protein structure
3d-explorer
SeqMan
Multiple alignment
Analysis of expression data
Plant promoter database
Search and map repeats
Extracting known SNPs

 

 

Comparison of genomic and protein sequences

EST_map / Mapping your mRNA/EST to Chromosome sequence of Human genome

Paste your sequence in here:

Alternatively, load a local file with sequence in Fasta format:
Local file name:

Please select:

Advanced options [see example of value in (..)]:

Split block (if possible).
Split block recursively (if possible).
Fine adjustment of block bounds.
Use consensus only for target sequence, if target sequence is profile.
Use consensus only for query sequence, if query sequence is profile.
Scoring methods for whole sequence. Score is: 1 – Maximum fragment score (default). 2 – All blocks score (default). 3 – Blast-like score.
Do not consider L-plets the number of which exceed this mathematical expectation.
Do not consider L-plets with low complexity (L-plets consist of poly tracts (AAAAA..., ATATATAT... etc.))
Output N best alignment (mainly non overlapped).
Output N best alternative alignment.
Output N best non overlapped alignment.
Output homology blocks only (not alignment)
Use group of symbols. N group numbers.
Alignment region on target sequence does not exсeed given length.
Alignment region on query sequence does not exceed given length.
Alignment region on target sequence does not exceed length of second sequence multiplied to N (N - is floating point number.
Alignment region on query sequence does not exceed length of first sequence multiplied to N (N - is floating point number).
Alignment region on second sequence does not exceed length of first sequence multiplied to N (N - is floating point number).
Alignment region on target sequence does not exceed length of second sequence plus N.
Alignment region on query sequence does not exceed length of first sequence plus N.
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.
Target sequence is prealigned profile.
Query sequence is prealigned profile.
Scan target sequence in different chain: 0 - In direct chain only (default). 1 - In reverse chain only. 2 - In both chains.
Scan query sequence in different chain: 0 - In direct chain only (default). 1 - In reverse chain only. 2 - In both chains.
Get target sequence from this position (default value 1).
Get target sequence to this position (0 - get to end, default value 0.
Get query sequence from this position (default value 1).
Get query sequence to this position (0 - get sequences to end, default value 0).
Options "Get target sequence from this position" and "Get target sequence to this position" are applied to complimentary chain of target sequence.
Options "Get query sequence from this position" and "Get query sequence to this position" are applied to complimentary chain of query sequence.
Remove trailing X symbols from target sequence.
Remove trailing X symbols from query ( or base) sequence.
Remove polyT head from target sequence.
Remove polyT head from query (or base) sequence.
Maximal length of readed name (default value 80), if = 0 full length.
Assume target sequence is preliminary complemented.
Assume query sequence is preliminary complemented.
Global alignment with tail gaps by dynamic programming.
Global alignment without tail gaps by dynamic programming.
Local alignment by dynamic programming.
To use step N on target sequence
To use step N on query sequence.
Output mode may be: 0 - Block info only (default). 1 - Blocks with sequences only. 2 (obsolete). 3 - Print alignment. This parameter ignore -s and -nbest parameters. 4 - Alignment bounds info only. 5 - Alignment bounds, Block info and alignment.
Use separator between lines of alignment.
Output alignment format (when "Output mode"=3 specified): 0 - Two line format (default). 1 - Four line format.
Print alignment for N symbols in each line (Default setting: 60).
Do not output unaligned flanks outside alignment.
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
Additionally print non translated sequence (when "Output mode"=2 or 3 specified).
Print alignment for N symbols in flank of alignment block (Default setting: 15).
This value will be added to target sequence numeration on output.
This value will be added to query sequence numeration on output.
Print progress information for each N processed base sequences.
Print progress information for each N processed base sequences to stderr.
Sort regions of homology by: 0 - No sorting (default). 1 - Location. 2 - Score.
Output alignment in HTML format.
N – html color value
Output alignment result just at alignment process. Default value - on.
Don’t print a header of result after sorting.
Do not verify accuransy of first exon.
No filters no splice site setting. Alignment as it is.
Do not filter inconsistent alignment, but process each alignment.
Use Some additional minor procedures for more precision.
Do not consider GC donor site.
Put here other options, if any.

[Help] [Hide advanced options
[Example]

Return to page with other programs of group: Alignment / Sequences & genomes


Your use of Softberry programs signifies that you accept Terms of Use

Last modification date: 24 Jul 2007

© 2020 www.softberry.com