FIMO Output
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Prashant Kumar
Oct 25, 2016, 7:03:37 PM10/25/16
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Hi All,
I used the command line version of FIMO.
fimo --oc . --verbosity 1 --bgfile E_coli_K12_MG1655.fna.bfile --thresh 1.0E-5 x.meme E_coli_K12_MG1655.fna
I don't get the same output as the website.I don't see the gene names for each matched result.
I downloaded the Ecoli .fna file from NCBI. Is FIMO using a different version?
Thanks,
Prashant
CharlesEGrant
Oct 25, 2016, 7:45:40 PM10/25/16
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Which database category did you select on the web form? For E Colil K12 MG1655 we provide both the full genome (under Genbank Bacteria Genomes and Proteins), and upstream sequences (under Upstream Sequences Prokaryotic). For all the online databases the source information can be found in the "Sequence Databases" section under the "Databases" menu in the side bar.
The full genome wouldn't be annotated with gene names, so I suspect you were looking at the "Upstream Sequences" category. We download the Prokaryotic upstream sequences from RSAT.
Prashant Kumar
Oct 25, 2016, 9:00:35 PM10/25/16
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Thanks a lot
Prashant Kumar
Oct 26, 2016, 12:06:25 PM10/26/16
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I downloaded the file from http://rsat-tagc.univ-mrs.fr/rsat/
and ran FIMO with the same command line syntax: I get output with the gene names this time.
But the website output is different and bigger than what I got with the command line syntax.
CharlesEGrant
Oct 26, 2016, 3:50:43 PM10/26/16
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Did you set the p-value threshold on the website to 1e-05 as you did your command line?
If so, please attach copies of the two FIMO outputs. That would help us diagnose the problem.
Prashant Kumar
Oct 26, 2016, 4:37:44 PM10/26/16
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Yes, I had set the p-value <= 1e-5
Website output:
#pattern name sequence name start stop strand score p-value q-value matched sequence 1 YP_026182.1|ascF 161 172 + 16.3761 2.59e-07 0.248 GTGAAACCGGTT 1 NP_417194.2|ascG 88 99 - 16.3761 2.59e-07 0.248 GTGAAACCGGTT 1 NP_417370.1|xerD 112 123 + 16.1743 4.6e-07 0.248 GTGAAACAGGAT 1 YP_026182.1|ascF 89 100 - 16.1651 5.1e-07 0.248 GTGAAACCGGTC 1 NP_417194.2|ascG 160 171 + 16.1651 5.1e-07 0.248 GTGAAACCGGTC 1 NP_416820.1|dedA 198 209 + 16.1651 5.1e-07 0.248 GTGAAACCGGTC 1 NP_417877.1|malT 272 283 + 15.6514 1.21e-06 0.442 GTGAAACAGTTT 1 YP_026218.1|malP 329 340 - 15.6514 1.21e-06 0.442 GTGAAACAGTTT 1 NP_417274.1|queF 61 72 + 15.5963 1.55e-06 0.501 GTGAAACATGTC 1 NP_418354.1|tpiA 34 45 - 15.2385 2.75e-06 0.687 GTGAAACAGTAT 1 NP_418175.3|yieL 132 143 + 15.2385 2.75e-06 0.687 GTGAAACAGTAT 1 NP_414879.3|lacI 77 88 + 15.1835 3.14e-06 0.687 GTGAAACCAGTA 1 YP_026189.1|yghJ 626 637 + 15.1835 3.14e-06 0.687 GTGAAACCTGAT 1 NP_415055.1|purK 1 12 + 15.0734 3.32e-06 0.687 ATGAAACAGGTT 1 NP_417020.1|fdx 72 83 + 15.0275 3.68e-06 0.687 GTGAAACCATTC 1 NP_414653.1|ampE 103 114 + 14.8716 4.29e-06 0.687 GTGAAACATTTT 1 NP_415901.2|ydbL 108 119 + 14.8716 4.29e-06 0.687 GTGAAACATTTT 1 NP_418735.2|fimI 248 259 - 14.8624 4.56e-06 0.687 ATGAAACCGGTT 1 NP_415276.1|gpmA 258 269 - 14.8624 4.56e-06 0.687 GTGAAACGGTTT 1 NP_416410.1|otsA 131 142 + 14.8073 5.31e-06 0.687 GTGAAACAGGGA 1 NP_417227.1|ispD 169 180 + 14.8073 5.31e-06 0.687 GTGAAACGTGTC 1 NP_415279.1|galT 74 85 - 14.7706 5.42e-06 0.687 GTGAAACCAGAA 1 NP_417074.1|grcA 485 496 + 14.7706 5.42e-06 0.687 GTGAAACCAGAA 1 NP_414698.1|erpA 219 230 - 14.6147 6.4e-06 0.713 GTGAAACCATAC 1 NP_416743.1|glpT 91 102 + 14.6055 6.72e-06 0.713 GTGAAACGTGAT 1 NP_417418.1|galP 114 125 - 14.6055 6.72e-06 0.713 GTGAAACGTGAT 1 NP_416744.1|glpA 171 182 - 14.6055 6.72e-06 0.713 GTGAAACGTGAT 1 NP_414790.1|insI1 222 233 + 14.4587 7.13e-06 0.713 GTGAAACAATTA 1 b4587|insN 222 233 + 14.4587 7.13e-06 0.713 GTGAAACAATTA 1 b1577|ydfE 19 30 - 14.4495 7.73e-06 0.713 ATGAAACCGGAT 1 NP_415006.1|htpG 146 157 + 14.2936 8.37e-06 0.713 GTGAAACAGCTT 1 NP_415419.2|ycaM 24 35 - 14.2477 9.05e-06 0.713 GTGAAACAGTAA 1 NP_414865.1|prpB 39 50 - 14.2477 9.05e-06 0.713 ATGAAACAAGAC 1 NP_416307.1|yoaF 77 88 + 14.2477 9.05e-06 0.713 ATGAAACAAGAC 1 NP_416308.4|yeaP 95 106 - 14.2477 9.05e-06 0.713 ATGAAACAAGAC 1 NP_414864.1|prpR 189 200 + 14.2477 9.05e-06 0.713 ATGAAACAAGAC 1 NP_416130.3|manA 359 370 - 14.2477 9.05e-06 0.713 GTGAAACGATAT 1 NP_416300.2|yeaJ 146 157 - 14.1927 9.58e-06 0.716 GTGAAACGAGAA 1 NP_417027.1|trmJ 236 247 + 14.1927 9.58e-06 0.716 GTGAAACCCGAC
Command Line Output:
#pattern name sequence name start stop strand score p-value q-value matched sequence 1 947154|ascF 89 100 - 16.7196 3.4e-08 0.0183 GTGAAACCGGTC 1 947305|ascG 160 171 + 16.7196 3.4e-08 0.0183 GTGAAACCGGTC 1 947305|ascG 88 99 - 16.6168 1.32e-07 0.0355 GTGAAACCGGTT 1 947154|ascF 161 172 + 16.6168 1.32e-07 0.0355 GTGAAACCGGTT 1 947921|malT 61 72 + 15.2617 2.37e-06 0.426 GTGAAACAGTTT 1 947922|malP 118 129 - 15.2617 2.37e-06 0.426 GTGAAACAGTTT 1 948409|tpiA 34 45 - 14.8505 4.61e-06 0.608 GTGAAACAGTAT 1 948035|yhjC 312 323 + 14.6822 5.26e-06 0.608 GTGAAACCCGGC 1 946704|glpT 91 102 + 14.5327 6.2e-06 0.608 GTGAAACGTGAT 1 947434|galP 91 102 - 14.5327 6.2e-06 0.608 GTGAAACGTGAT 1 946713|glpA 171 182 - 14.5327 6.2e-06 0.608 GTGAAACGTGAT 1 946113|ydfE 19 30 - 14.3738 7.57e-06 0.68 ATGAAACCGGAT 1 946290|yeaJ 146 157
CharlesEGrant
Oct 27, 2016, 1:29:09 PM10/27/16
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I'm not sure what you downloaded. It is similar, but clearly not exactly the same set of sequences as our online database.
The MEME Suite web site uses the RSAT programatic API to download the upstream sequences. The database download source code we use can be found in the MEME Suite source distribution under the Projects/meme-trunk/website/src/au/edu/uq/imb/memesuite/updatedb directory. We don't provide assistance in running this program locally though.
However, you should be able to use the RSAT web interface to get the same data.
Go to the RSAT Prokaryotes web page. Click on the "Sequence Tools", choose "retreive sequence", select your organism, click "All" in the "Genes" radio button, click the "CDS" radio button for the "Reference feature type", select "upstream" as the sequence type, set "from" to -1000 and "to" to "200". Finally, set the "Sequence label" to "gene identifier + name", then click on the "GO" button.
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