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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<title>Manual</title>
</head>
<body>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<p style="margin-bottom: 0in; line-height: 100%"><big><big><big><b>Documentation</b></big></big></big></p>
<p style="margin-bottom: 0in; line-height: 100%"><br>
<a href="smorgas2.mp4">Video Tutorial</a>.<br>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><br>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><b>1. Installation</b></p>
<p style="margin-bottom: 0in; line-height: 100%"><b>1.1. Clone the
repository</b> </p>
<p style="margin-bottom: 0in; line-height: 100%">To get the source
code and compile it, type: </p>
<p style="margin-bottom: 0in; line-height: 100%">> git clone <a
href="https://github.com/nedaz/Smorgas-proteins.git">https://github.com/nedaz/Smorgas-proteins.git</a>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><br>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><b>1.2. Build
executables</b></p>
<p style="margin-bottom: 0in; line-height: 100%">> cd
Smorgas-proteins<br>
</p>
<p style="margin-bottom: 0in; line-height: 100%">> make</p>
<p style="margin-bottom: 0in; line-height: 100%"><br>
</p>
<b>2. Prepare your protein database</b>
<p style="margin-bottom: 0in; line-height: 100%">Smörgås reads the
database in multi-fasta format. For smaller databases (<300K
entries), you can supply the entire file. For larger databases, we
recommend to split the file into equal-sized chunks, which will
both reduce memory usage, as well as allowing for parallel
processing. You can split the database by typing </p>
<p style="margin-bottom: 0in; line-height: 100%">> SplitFasta -i
<database.fasta> -n <how many chunks you would like> </p>
<p style="margin-bottom: 0in; line-height: 100%">Please note that
the number of chunks must match the number of processes you use
for parallel runs. </p>
<p style="margin-bottom: 0in; line-height: 100%"><br>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><b>3. Run in batch
mode</b></p>
<p style="margin-bottom: 0in; line-height: 100%"><b>3.1 Help screen
and arguments</b> </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> Type: </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> > ./runSatsumaProt </p>
<p style="margin-bottom: 0in; line-height: 100%">to bring up the
following help: </p>
<p style="margin-bottom: 0in; line-height: 100%">./runSatsumaProt:
Satsuma-based (cross-correlation) protein alignment tool. </p>
<p style="margin-bottom: 0in; line-height: 100%">Available
arguments: </p>
<p style="margin-bottom: 0in; line-height: 100%">-t<string> :
target protein fasta (def=)<br>
-q<string> : query protein fasta</p>
-db<string> : protein database in Spines binary format (def=)<br>
-e<bool> : exhaustive search (no filtering) (def=0)<br>
-k<int> : k-mer size (def=4)<br>
-kmerStep<int> : Step size to be used in generating
filteration kmers (def=1)<br>
-filter<int> : Type of prefilter of hits to use- 1:fixed
distance k-mer based 2:max k-mer based (def=1)<br>
-allowFails<int> : Number of failures to allow before stopping
the search (def=50)<br>
-E-value<double> : show only alignments with better E-value
(def=0.01)<br>
-self<bool> : self-alignments (def=0)<br>
-same<bool> : same alignments (def=0)<br>
-block<int> : search only this subset (requires -e) (def=0)<br>
-n_blocks<int> : number of blocks (w/ -e) (def=0)<br>
-rna<bool> : Do RNA alignments (def=0)<br>
-timestamps<bool> : Print time stamps (def=0)<br>
-m<int> : number of results to display (def=50)<br>
-cutoff<double> : show only alignments at this (ingapped)
identity or higher (def=0)<br>
-wSlide<int> : Filter Window slide, if set to 1 the window
sliding will cover all kmers. (def=2)<br>
-l<string> : Application logging file (def=application.log)
<p style="margin-bottom: 0in; line-height: 100%"><br>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><b>3.2 Running the
aligner</b></p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> For using the default options, type:</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> > runSatsumaProtein -t <protein database> -q
<query fasta file> > <output file> & </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> The output will be written to stdout in human-readable
format, including statistics and a summary line, e.g.: </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
<font face="Courier New, Courier, monospace" size="-1">**********************************************</font></p>
<font face="Courier New, Courier, monospace" size="-1"></font><font
face="Courier New, Courier, monospace" size="-1">Target sequence
size: 368</font><font face="Courier New, Courier, monospace"
size="-1"></font><font face="Courier New, Courier, monospace"
size="-1"><br>
Query sequence size: 757</font><font face="Courier New, Courier,
monospace" size="-1"><br>
Target offset: 1</font><font face="Courier New, Courier,
monospace" size="-1"><br>
Query offset: 200</font><font face="Courier New, Courier,
monospace" size="-1"><br>
Target aligned basepairs: 366</font><font face="Courier New,
Courier, monospace" size="-1"><br>
Query aligned basepairs: 416</font><font face="Courier New,
Courier, monospace" size="-1"><br>
Raw Score: -1</font><font face="Courier New, Courier, monospace"
size="-1"><br>
Identity score: 0.507212</font><font face="Courier New, Courier,
monospace" size="-1"><br>
Total Edit Count 171</font><font face="Courier New, Courier,
monospace" size="-1"><br>
Mean Contiguity length 0</font><font face="Courier New, Courier,
monospace" size="-1"><br>
Mod-Smith-waterman score: -2</font><font face="Courier New,
Courier, monospace" size="-1"><br>
Significance P-value: 1</font><font face="Courier New, Courier,
monospace" size="-1"><br>
***********************************************</font><font
face="Courier New, Courier, monospace" size="-1"> </font>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"><font face="Courier New, Courier, monospace" size="-1">
Query: 200
LMNNSTGRSHVLAHPTGIDTIARSLAADNIKTKIAALEILGAVCLVPGGHKKVLTAMLNYQEYAAERARFQGIVNDLDKS
279</font></p>
<font face="Courier New, Courier, monospace" size="-1"></font><font
face="Courier New, Courier, monospace" size="-1">
LMNNS GR+HVL+H I+ IA+SLA +NIKTK+A LEI+GAVCLVPGGH+K+L AML+YQ++A ER
RFQ ++NDLD+S</font><font face="Courier New, Courier, monospace"
size="-1"></font><font face="Courier New, Courier, monospace"
size="-1"><br>
Sbjct: 1
LMNNSQGRAHVLSHSESINIIAQSLATENIKTKVAVLEIMGAVCLVPGGHRKILEAMLHYQKFACERTRFQTLLNDLDRS
80</font><font face="Courier New, Courier, monospace" size="-1"> </font>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <font face="Courier New, Courier, monospace" size="-1"><br>
</font> </p>
<font face="Courier New, Courier, monospace" size="-1"> </font>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"><font face="Courier New, Courier, monospace" size="-1">
Query: 280
TGAYRDDVNLKTAIMSFINAVLNYGPGQENLEFRLHLRYEFLMLGIQPVIDKLRKHENETLNRHLDFFEMVRNEDEKELA
359</font></p>
<font face="Courier New, Courier, monospace" size="-1"></font><font
face="Courier New, Courier, monospace" size="-1">
TG YRD+V+LKTAIMSFINA+L+ G G+ +LEFR+HLRYEFLMLGIQP+IDKLR H+N
TL+RHLD+FEM+RN+DE LA</font><font face="Courier New, Courier,
monospace" size="-1"><br>
Sbjct: 81
TGRYRDEVSLKTAIMSFINAILSQGAGETSLEFRVHLRYEFLMLGIQPIIDKLRSHDNATLDRHLDYFEMLRNDDELALA
160</font><font face="Courier New, Courier, monospace" size="-1">
</font>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <font face="Courier New, Courier, monospace" size="-1"><br>
</font> </p>
<font face="Courier New, Courier, monospace" size="-1"> </font>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> </p>
<font face="Courier New, Courier, monospace" size="-1"></font>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"><font face="Courier New, Courier, monospace" size="-1">
Query: 360
RKFNHEHVDTKSATAMFDLLRRKLSHSGAYPHLLSLLQHLLLLPHGG--PNAQHWLMFDRVVQQIVLQQEERPTSEIIDP
437</font></p>
<font face="Courier New, Courier, monospace" size="-1"></font><font
face="Courier New, Courier, monospace" size="-1">
R+F H+DTKSA+ +FDL+R+K++H+ AYPH +S+L H LL+PH Q+WL+ DR+VQQ+VLQ +</font><font
face="Courier New, Courier, monospace" size="-1"><br>
Sbjct: 161
RRFESVHIDTKSASQVFDLIRKKMNHTDAYPHFMSVLHHCLLMPHKRSGNTVQYWLLLDRIVQQMVLQ--NDKGHDPDVT
238</font><font face="Courier New, Courier, monospace" size="-1">
</font>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <font face="Courier New, Courier, monospace" size="-1"><br>
</font> </p>
<font face="Courier New, Courier, monospace" size="-1"> </font><font
face="Courier New, Courier, monospace" size="-1"> </font><font
face="Courier New, Courier, monospace" size="-1"></font><font
face="Courier New, Courier, monospace" size="-1">Summary Seq_504
vs.
UniRef90_B0W4A3_Disheveled-associated_activator_of_morphogenesis_2_n=1_Tax=Culex_quinquefasciatus_RepID=B0W4A3_CULQU
score:
4.83175e-07 q-coords: 200 616 t-coords: 1 367 0.507212 4.83175e-07</font>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"><font face="Courier New, Courier, monospace" size="-1"> </font><br>
</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> Note that the summary line appears after the alignment. </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><b>3.3 Adjusting
parameters for parallel run</b></p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> Consider lowering the -m option (number of alignments to
report) to increase speed, e.g. if the desired number of
alignments in the end is 50, and the program runs in 24 processes,
you might set -m to 10.</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><b>3.4 Interpret
the output</b></p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
Note that Smörgås doe not print alignments in sorted format. To sort
the results (summary line only), use:
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> > SortSmorgasOut -i <result file> -c <maximum #
of alignments per query sequence> > <sorted output> </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> Note that the option -f, which defaults to 0.1, applies an
additional f-vale threshold. </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> For results from parallel runs, concatenate the output and
run SortSmorgasOut. </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
<p style="margin-bottom: 0in; line-height: 100%"><b>4. Run the web
server</b></p>
<p style="margin-bottom: 0in; line-height: 100%"><b>4.1 Data files</b></p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> Smorgas needs a number of files to run a web server. All
these files can be found in the smorgas_server_data/ directory,
and must be located where the programs are executed. In this
directory, there are also a few sample scripts (run_fp,
run_plants, run_te), as well as some small databases. </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> To manually start the server, cd into the directory and
run: </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> > ../SmorgasCommLayer -f refseq/refseq_plants.faa
-server localhost > scl.out &<br>
</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%">> ../TangerineServer -t taxonomy.txt -col
plant_colors.txt > ts.out &</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> which intializes the server with the refseq plant database,
instructs the server that both the communication layer, which
controls the processes, as well as the web server run on the same
physical machine (localhost). </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> **** IMPORTANT *****: Please wait until the ProtServer
processes are initialized (i.e. their CPU usage drops to 0)
before using the service!! This should take less than a few
minutes.</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> Please note that the supplied taxonomy.txt file (derived
from the NCBI taxonomy database) is not current and should be
updated. </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> Supply your custom colors for display using the -col option
(it will use defaults if not specified). </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> To parallelize the database, supply a configuration file
using the -c option: </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> ../SmorgasCommLayer -c <your config file> -server
localhost > scl.out & </p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> The configuration file is a simple text files with two
entries per line, a name, and a location of the fasta file, e.g.:
</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
nr00 /references/databases/nr/2014_09_15/nr.fasta.0<br>
nr01 /references/databases/nr/2014_09_15/nr.fasta.1<br>
nr02 /references/databases/nr/2014_09_15/nr.fasta.2<br>
nr03 /references/databases/nr/2014_09_15/nr.fasta.3
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> The communication layer will launch a number of ProtServer
instances accoring to the number of entries in the config file.</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
<p style="margin-bottom: 0in; font-weight: normal; line-height:
100%"> <br>
</p>
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