FMAP - Super-fast search of query sequence over human genome
webmaster_softberry_com at acedsl.com
webmaster_softberry_com at acedsl.com
Thu Dec 13 08:17:18 EST 2001
FMAP - Super-fast search of query sequence over human genome.
It takes FMAP less than a second to map a sequence on a genome.
Splice site recognition feature allows FMAP
http://www.softberry.com/showmap.html
to accurately map multi-exon ESTs and mRNAs.
It aligns splice sites on Go to our human genome mapping page to try the
program on human
genome draft. Alternatively, you can map a sequence in
Softberry Genome Explorer http://www.softberry.com/genomb/chrvis.htmland
immediately see a lot of information about mapped site - known and predicted
genes,
ESTs, predicted promoters and other.
FMAP - Program for fast alignment of your sequence to Genome sequence
Web version of FMAP program is running with strong parameters, its local
execution requires < 1 sec for finding alignments of your sequence with Human
genome
about 3 GB. Version with very accurate alignment and more sensitive search -
RUN Fmap+Scan2.
To map your RNA or EST sequence USE Fmap+EST_MAP combination which will take
into account
splice sites characteristics to select optimal alignment. Program has several
ouput
formats one of which is presented in WEB results.
--------------------------------------------------------------------------------
FMAP output:
p Wed Jul 18 23:24:14 EDT 2001
[DD] Sequence: 1, S: 600, L:5805 C9001122 in chr1
Summ of block lengths: 135, Alignment bounds:
On first sequence: start 104888252, end 104888386, length 135
On second sequence: start 4226, end 4360, length 135
Block of alignment: 1
1 P: 104888252 4226 L: 135, G: 81.481, W: 600, S:600
1 11 104888238 104888248 104888258 104888268
aattctttgattgat(..)ggccctgctgcaggcTGACCACTTCAGTGGATGCTGTGGTT
---------------(..)cagaggtggctctgaTGACCACATCAGTGGATGTCCTTGTG
4211 4211 4212 4222 4232 4242
104888278 104888288 104888298 104888308 104888318 104888328
GCCATCTGCGTGATTTTCTCCATGTCCTTCGTCCCAGCCAGCTTTGTCCTTTATTTGATC
TCCATCTGTGTCATCTTTGCAATGTCCTTCGTCCCAGCCAGCTTTGTCGTATTCCTGATC
4252 4262 4272 4282 4292 4302
104888338 104888348 104888358 104888368 104888378 104888388
CAGGAGCGGGTGAACAAATCCAAGCACCTCCAGTTTATCAGTGGAGTGAgccccaccacc
CAGGAGCGGGTCAGCAAAGCAAAACACCTGCAGTTCATCAGTGGAGTGAagcctgtcatc
4312 4322 4332 4342 4352 4362
104888398 276020454 276020464
tact(..)aaccagatctcatga
tact(..)---------------
4372 5806 5806
[DR] Sequence: 2, S: 2490, L:5805 C9001122 in chr9
Summ of block lengths: 5777, Alignment bounds:
On first sequence: start 106389262, end 106448770, length 59509
On second sequence: start 1, end 5805, length 5805
Block of alignment: 40
1 P: 106389262 1 L: 138, G: 100.000, W: 1380, S:1380
2 P: 106390340 139 L: 249, G: 100.000, W: 2490, S:2490
3 P: 106391247 388 L: 91, G: 100.000, W: 910, S:910
4 P: 106391820 479 L: 103, G: 100.000, W: 1030, S:1030
5 P: 106392866 582 L: 134, G: 100.000, W: 1340, S:1340
6 P: 106393371 716 L: 146, G: 100.000, W: 1460, S:1460
7 P: 106395871 862 L: 107, G: 100.000, W: 1070, S:1070
8 P: 106396885 969 L: 61, G: 100.000, W: 610, S:610
9 P: 106397733 1030 L: 121, G: 100.000, W: 1210, S:1210
10 P: 106398118 1151 L: 131, G: 100.000, W: 1310, S:1310
11 P: 106399335 1282 L: 123, G: 100.000, W: 1230, S:1230
12 P: 106401622 1405 L: 178, G: 100.000, W: 1780, S:1780
13 P: 106403020 1583 L: 172, G: 100.000, W: 1720, S:1720
14 P: 106403713 1755 L: 72, G: 100.000, W: 720, S:720
15 P: 106405254 1827 L: 112, G: 100.000, W: 1120, S:1120
16 P: 106407827 1967 L: 95, G: 100.000, W: 950, S:950
17 P: 106409442 2062 L: 190, G: 100.000, W: 1900, S:1900
18 P: 106412667 2252 L: 99, G: 100.000, W: 990, S:990
19 P: 106414001 2351 L: 125, G: 100.000, W: 1250, S:1250
20 P: 106415775 2476 L: 152, G: 100.000, W: 1520, S:1520
21 P: 106417322 2628 L: 115, G: 100.000, W: 1150, S:1150
22 P: 106417632 2743 L: 45, G: 100.000, W: 450, S:450
23 P: 106419344 2788 L: 204, G: 100.000, W: 2040, S:2040
24 P: 106420534 2992 L: 71, G: 100.000, W: 710, S:710
25 P: 106421863 3063 L: 224, G: 100.000, W: 2240, S:2240
26 P: 106422789 3287 L: 133, G: 100.000, W: 1330, S:1330
27 P: 106423125 3420 L: 146, G: 100.000, W: 1460, S:1460
28 P: 106424576 3566 L: 130, G: 100.000, W: 1300, S:1300
29 P: 106425695 3696 L: 174, G: 100.000, W: 1740, S:1740
30 P: 106427666 3870 L: 113, G: 100.000, W: 1130, S:1130
31 P: 106428883 3983 L: 206, G: 100.000, W: 2060, S:2060
32 P: 106430149 4189 L: 224, G: 100.000, W: 2240, S:2240
33 P: 106432119 4413 L: 221, G: 100.000, W: 2210, S:2210
34 P: 106434126 4634 L: 174, G: 100.000, W: 1740, S:1740
35 P: 106434820 4808 L: 211, G: 100.000, W: 2110, S:2110
36 P: 106435777 5019 L: 197, G: 100.000, W: 1970, S:1970
37 P: 106440182 5216 L: 114, G: 100.000, W: 1140, S:1140
38 P: 106440627 5330 L: 142, G: 100.000, W: 1420, S:1420
39 P: 106443480 5472 L: 243, G: 100.000, W: 2430, S:2430
40 P: 106448680 5715 L: 91, G: 100.000, W: 910, S:910
1 11 106389248 106389258 106389268 106389278
gaattcctggtggag(..)tatgaacaggattctTCATACATAGCTTTCTTTCACTTTCT
---------------(..)---------------TCATACATAGCTTTCTTTCACTTTCT
1 1 1 1 7 17
106389288 106389298 106389308 106389318 106389328 106389338
CATCCTGTAGAAAAGATGTGAGAACTGCAACGTCCACTACTGTCTGGTTTTTGTGTAATG
CATCCTGTAGAAAAGATGTGAGAACTGCAACGTCCACTACTGTCTGGTTTTTGTGTAATG
27 37 47 57 67 77
106389348 106389358 106389368 106389378 106389388 106389398
AGAGGTCTTTTAAGTGGTCATCATCACTTTGGTCCTTGGCAAAGTTCACAAAtacctgtt
AGAGGTCTTTTAAGTGGTCATCATCACTTTGGTCCTTGGCAAAGTTCACAAA--------
87 97 107 117 127 137
106389408 106390325 106390334 106390344 106390354 106390364
aaaagat(..)ttgacactcaaagctTACTTGGTCAAGTGTTGTCTGAGAAACAGAGTAG
-------(..)---------------TACTTGGTCAAGTGTTGTCTGAGAAACAGAGTAG
139 139 139 143 153 163
106390374 106390384 106390394 106390404 106390414 106390424
TCTTCTATGTGGAGTCGCTTTTTGCTCTGGGAGAGGATGCTGAATATCCTGGCCAGAGAA
TCTTCTATGTGGAGTCGCTTTTTGCTCTGGGAGAGGATGCTGAATATCCTGGCCAGAGAA
173 183 193 203 213 223
106390434 106390444 106390454 106390464 106390474 106390484
GATAATGAAGATGGAAGCTGGTATTGTAGCATGTTCCGGTGTTTCTCTTTTAGAACACTT
GATAATGAAGATGGAAGCTGGTATTGTAGCATGTTCCGGTGTTTCTCTTTTAGAACACTT
233 243 253 263 273 283
106390494 106390504 106390514 106390524 106390534 106390544
CCAGGAAATGCAAGTCCAAAGAAATCCTGGACAGGCTTCAGGTCCGGGTTGGACCCTGCT
CCAGGAAATGCAAGTCCAAAGAAATCCTGGACAGGCTTCAGGTCCGGGTTGGACCCTGCT
293 303 313 323 333 343
106390554 106390564 106390574 106390584 106390594 106391232
ATTCGTACAACTATTGTATAACCATCTCCAAACCTgaaagcaggaaaaaa(..)ttatct
ATTCGTACAACTATTGTATAACCATCTCCAAACCT---------------(..)------
353 363 373 383 388 388
106391238 106391248 106391258 106391268 106391278 106391288
ttattacctATTTTTTAGATGCTGGACACTGCCAAGGCACCTGAACCTTCCATTGACCAT
---------ATTTTTTAGATGCTGGACACTGCCAAGGCACCTGAACCTTCCATTGACCAT
388 389 399 409 419 429
106391298 106391308 106391318 106391328 106391338 106391348
GATTGCCATCCTAGTGCAAAGAGCTTCACATTCTTCCATActgcggtaaaacaga(..)g
GATTGCCATCCTAGTGCAAAGAGCTTCACATTCTTCCATA---------------(..)-
439 449 459 469 479 479
-------------------------------------------------
This mail sent through AceDSL WebMail (http://webmail.acedsl.com)
---
More information about the Bio-soft
mailing list
Send comments to us at biosci-help [At] net.bio.net
