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EMBOSS: supermatcher |
supermatcher ~/wordtest/U68037 ~/wordtest/AB003171 -noscoreonly Finds a match of a large sequence against one or more sequences Gap opening penalty [10.0]: Gap extension penalty [0.5]: 3.0 Output file [stdout]: Local: RNU68037 vs EM:AB003171 Score: 30.00 RNU68037 820 tcaaccacagctgccctccgcagctctcggggag.gcggc.tccg 862 ||||| |||| || | |||| |||||| || | ||| EM:AB003171 2492 tcaactacag.aaccatgtgcag....aggggagagctccatcct 2531 RNU68037 863 cgcgcagggttcacgcacacga.cgtgg.aaatggtgggccagct 905 | || ||| | || || || | ||| || |||| | | EM:AB003171 2532 tgaaca..gttaaagc.ca.gagcttggtaacaagtggataaatt 2572 RNU68037 906 .cgtgggcatcatggtggtgtc.gtg..catctgctggagc 942 | | ||||| || ||| | | || ||| |||| EM:AB003171 2573 acat....atcattttgcggtctgagaacacatgc.agagc 2608
Mandatory qualifiers: [-seqa] seqall Sequence database USA [-seqb] seqset Sequence set USA -gapopen float Gap opening penalty -gapextend float Gap extension penalty -outfile align (no help text) align value Optional qualifiers: -datafile matrixf Matrix file -errorfile outfile Error file to be written to -width integer Alignment width -wordlen integer word length for initial matching Advanced qualifiers: (none) General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-seqa] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-seqb] (Parameter 2) |
Sequence set USA | Readable sequences | Required |
-gapopen | Gap opening penalty | Number from 1.000 to 100.000 | 10.0 for any sequence type |
-gapextend | Gap extension penalty | Number from 0.100 to 10.000 | 0.5 for any sequence type |
-outfile | (no help text) align value | Alignment file | |
Optional qualifiers | Allowed values | Default | |
-datafile | Matrix file | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
-errorfile | Error file to be written to | Output file | supermatcher.error |
-width | Alignment width | Any integer value | 16 |
-wordlen | word length for initial matching | Integer 3 or more | 6 |
Advanced qualifiers | Allowed values | Default | |
(none) |
Because it does a Smith & Waterman alignment (albeit in a narrow region around the diagonal shown to be the 'best' by a word match), this program can use huge amounts of memory if the sequences are large.
Because the alignment is made within a narrow area each side of the 'best' diagonal, if there are sufficient indels between the two sequences, then the path of the Smith & Waterman alignment can wander outside of this area. Making the width larger can avoid this problem, but you then use more memory.
The longer the sequences and the wider the specified alignment width, the more memory will be used.
If the program terminates due to lack of memory you can try the following:
Run the UNIX command 'limit' to see if your stack or memory usage have been limited and if so, run 'unlimit', (e.g.: '% unlimit stacksize').
Program name | Description |
---|---|
matcher | Finds the best local alignments between two sequences |
seqmatchall | Does an all-against-all comparison of a set of sequences |
water | Smith-Waterman local alignment |
wordmatch | Finds all exact matches of a given size between 2 sequences |