Introductory Unix

7/31/2019 Introductory Unix

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Unix Introduction(with a few bioinformatics examples)

Philippe GautierMRC - Human Genetics Unit

Bioinformatics Service


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Introductory UNIX for sequence analysis

http://wikilocal.hgu.mrc.ac.uk/Bioinformatics/wiki/index.php/UNIX

http://unixhelp.ed.ac.uk/

http://www.ee.surrey.ac.uk/Teaching/Unix/index.html

[email protected],

19 October 2001
http://wwwlocal.hgu.mrc.ac.uk/Computing/Helpsyst/UNIXhelp/index.htmlhttp://unixhelp.ed.ac.uk/http://www.ee.surrey.ac.uk/Teaching/Unix/index.htmlmailto:[email protected]:[email protected]://www.ee.surrey.ac.uk/Teaching/Unix/index.htmlhttp://unixhelp.ed.ac.uk/http://wwwlocal.hgu.mrc.ac.uk/Computing/Helpsyst/UNIXhelp/index.html


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Unix access (MRC):

Unix work station (solaris)

Pc telnet/Exceed/PuTTY. Connect to a Sunhost/server: glengoyne, coleburn, ladyburn,

strathisla use a ssh protocol (see computing for help)

Same username and password as for PCaccess (MRC)

Environment: command line NOT point andclick.

Mouse: 3 buttons functions/others variants


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Operating systems, shells, ...

the operating system is the flavor of unix

you use: Sun Solaris, GNU/Linux, MacOS X

A shell is a program that waits for you to type

a command and then executes it.

2 big families of shells with slight

differences: the C shells (csh tcsh) and the

Bourne shell (bash, ksh) echo $SHELL

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File systems

to know where you are: pwd

Root directory = your H: drive.

File hierarchy/tree:Root:

/net/homehost/export/home/usernameor ~username

Subdirectories:

/net/homehost/export/data/username/or ~username/data

net

homehost

export

home data

user1 user2 user1 user2


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Entering commands

type the command, then return

tips:

to go back to previously entered commands,use the up and down arrows

to auto-complete file names, use the tab key

if you are stuck within a

command/process/program, try ctrl-c toterminate it

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Unix commands:

Help/manuals: man Moving around:

cd, cd ., cd ..

pwd

ls, ls -ltr

more, less, cat

Manipulating files and directories:

mv, rm, cp, mkdir, rmdir Running scripts:

Scriptname (-parameters), with or without fullpath

Stopping running scripts: control-c


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Common commands: lsgogo$ ls

Pax6 all-hr.aln RepeatMasker

ensembl2008.ppt ian_repeat WT1

interactions.txt

gogo$ ls -l

total 89520

drwxr-xr-x 4 gogo staff 136 1 Dec 19:07 Pax6

drwxr-xr-x@ 43 gogo staff 1462 3 Oct 19:18 RepeatMasker

drwxr-xr-x 2 gogo staff 68 1 Dec 19:06 WT1

-rwx------ 1 gogo staff 82593 4 Nov 15:35 all-hr.aln

-rw-r--r-- 1 gogo staff 6077952 21 Nov 14:07 ensembl2008.ppt

drwxr-xr-x 31 gogo staff 1054 31 Oct 15:11 ian_repeat

-rw-r--r--@ 1 gogo staff 4624 21 Oct 14:47 interactions.txt

gogo$ ls -ltr

total 89520

drwxr-xr-x 5 gogo staff 170 3 Oct 18:21 testdir

drwxr-xr-x@ 43 gogo staff 1462 3 Oct 19:18 RepeatMasker

-rw-r--r--@ 1 gogo staff 4624 21 Oct 14:47 interactions.txt

drwxr-xr-x 31 gogo staff 1054 31 Oct 15:11 ian_repeat

-rwx------ 1 gogo staff 82593 4 Nov 15:35 all-hr.aln

-rw-r--r-- 1 gogo staff 6077952 21 Nov 14:07 ensembl2008.ppt

drwxr-xr-x 2 gogo staff 68 1 Dec 19:06 WT1

drwxr-xr-x 4 gogo staff 136 1 Dec 19:07 Pax6

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Common commands: pwd/cdgogo$ pwd

/Users/gogo

gogo$ cd Bioinfo/

gogo$ pwd

/Users/gogo/Bioinfo

gogo$ ls

Pax6 all-hr.aln snp_summary.pages

RepeatMasker ensembl2008.ppt testdir

RepeatMasker-open-3-2-6.tar ian_repeatWT1 interactions.txt

gogo$ cd Pax6/

gogo$ pwd

/Users/gogo/Bioinfo/Pax6

gogo$ cd

gogo$ pwd

/Users/gogo

gogo$ cd Bioinfo/Pax6 or cd /Users/gogo/Bioinfo/Pax6

gogo$ pwd

/Users/gogo/Bioinfo/Pax6

gogo$ cd ../

gogo$ pwd/Users/gogo/Bioinfo/

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Common commands: more, less, cat

glengoyne% lsfile2 file3 temp

glengoyne% more file2

file2 content

2222222222222222222


file3 content

3333333333333333

glengoyne% cat file2 file3

file2 content

2222222222222222222

file3 content

3333333333333333

glengoyne% cat file2 file3>file4


file2 content

2222222222222222222

file3 content

3333333333333333

glengoyne%

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Common commands: mv, cp, mkdir

glengoyne% ls

ex3list.txt file1 file2 file3 file4

glengoyne% cp file1 file5

glengoyne% ls


file5

glengoyne% mv file1 file6

glengoyne% ls


file6

glengoyne% mkdir ../testdir3

glengoyne% ls ../testdir3

glengoyne% mv file3 ../testdir3

glengoyne% cd ../testdir3

glengoyne% ls

file3

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Editing / creating files

Unix text editors: nano, emacs, vi

Microsoft word: save as .txt !!

grep

Batch actions

Use of wildcards foreach loop

Pipes |

>

>>

Other

&, top, lpr, acroread


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Example: use of wildcard

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Want to copy all ab1 files for exon 3.


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Example: use of wildcard

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$ lsA12_R14B12_SOX2_ex3_R_002.ab1 C12_R14B12_SOX2_ex5_R_004.ab1

E12_R14B12_SOX2_ex3_R_002.ab1

A12_R14B12_SOX2_ex3_R_002.seq C12_R14B12_SOX2_ex5_R_004.seq E12_R14B12_SOX2_ex3_R_002.seq

B12_R14B12_SOX2_ex5_R_004.ab1 D12_R14B12_SOX2_ex3_R_002.ab1 F12_R14B12_SOX2_ex3_R_002.ab1

B12_R14B12_SOX2_ex5_R_004.seq D12_R14B12_SOX2_ex3_R_002.seq F12_R14B12_SOX2_ex3_R_002.seq

C12_R14B12_SOX2_ex3_R_002.ab1 D12_R14B12_SOX2_ex5_R_006.ab1

C12_R14B12_SOX2_ex3_R_002.seq D12_R14B12_SOX2_ex5_R_006.seq

$ ls *ex3*ab1A12_R14B12_SOX2_ex3_R_002.ab1 D12_R14B12_SOX2_ex3_R_002.ab1

F12_R14B12_SOX2_ex3_R_002.ab1

C12_R14B12_SOX2_ex3_R_002.ab1 E12_R14B12_SOX2_ex3_R_002.ab1

Be very careful using wildcard! e.g.: rm * will erase all you files!


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other example: use of redirect

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Create a text file containing a list of file namesgogo$ lsA12_R14B12_SOX2_ex3_R_002.ab1 C12_R14B12_SOX2_ex5_R_004.ab1

E12_R14B12_SOX2_ex3_R_002.ab1

A12_R14B12_SOX2_ex3_R_002.seq C12_R14B12_SOX2_ex5_R_004.seq E12_R14B12_SOX2_ex3_R_002.seq

B12_R14B12_SOX2_ex5_R_004.ab1 D12_R14B12_SOX2_ex3_R_002.ab1 F12_R14B12_SOX2_ex3_R_002.ab1

B12_R14B12_SOX2_ex5_R_004.seq D12_R14B12_SOX2_ex3_R_002.seq F12_R14B12_SOX2_ex3_R_002.seq

C12_R14B12_SOX2_ex3_R_002.ab1 D12_R14B12_SOX2_ex5_R_006.ab1

C12_R14B12_SOX2_ex3_R_002.seq D12_R14B12_SOX2_ex5_R_006.seqgogo$ ls *ex3*ab1A12_R14B12_SOX2_ex3_R_002.ab1 D12_R14B12_SOX2_ex3_R_002.ab1

F12_R14B12_SOX2_ex3_R_002.ab1

C12_R14B12_SOX2_ex3_R_002.ab1 E12_R14B12_SOX2_ex3_R_002.ab1

gogo$ ls *ex5*seqB12_R14B12_SOX2_ex5_R_004.seq C12_R14B12_SOX2_ex5_R_004.seq

D12_R14B12_SOX2_ex5_R_006.seq

gogo$ ls *ex5*seq>ex5_sequences_list

gogo$ more ex5_sequences_listB12_R14B12_SOX2_ex5_R_004.seq

C12_R14B12_SOX2_ex5_R_004.seq

D12_R14B12_SOX2_ex5_R_006.seq

h l fil


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another example: concatenate files

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Concatenate files into a single one (for e.g., put sequences in a

unique file for use with an alignment program like Clustal)gogo$ ls *pax6.pepall_pax6.pep lineus_pax6.pep

saccoglossum_pax6.pep

branchiostoma_bel_pax6.pep ljap_pax6.pep strongylocentrotus_pax6.pep

branchiostoma_flo_pax6.pep loligo_pax6.pep

euprymna_pax6.pep platynereis_pax6.pepgogo$ cat *pax6.pep>all_pax6.pepgogo$

more all_pax6.pep>gi|117650666|gb|ABK54278.1| Pax6 [Branchiostoma belcheri]

MGRGHSGVNQLGGVFVNGRPLPDSTRQKIVELAHQGARPCDISRLLQVSNGCVSKILGRYYETGSIRPRA

IGGSKPRVATPEVVAKIAQFKRECPSIFAWEIRDRLLSEGICTNENIPSVSSINRVLRNLASGEKNTLQS

LQSADPQMLEKLRLLNGNAWPHPGPWPYPPATAGAPPPQTNGNVTTKKEGDGKLASQILTLHGYQDQGDGSNDDSDEAQARLRLKRKLQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR

AKWRREEKLRNQRRSQDSDSSSPSRIPISSSFSTATMYQPIAPPSAPVMSRSSHAGLTDSYSSLPPVPSF

SVPGNMAPMPSMQQSREQTSYSCMIPHSTAMTPRGYDSLALGSYNPTHAGHHVTTTHPSHMQAPSMTGHS

HMTHANGGSAGLISPGVSVPVQVPGAVTEEMTSQPYWPRIQ

>gi|3204110|emb|CAA11364.1| Pax6 [Branchiostoma floridae]

MPHKAWTLQRPADEHAQYSPVQADPGHSGVNQLGGVFVGGRPLPDSTRRKIVELAHQGARPCDISRLLQV

SNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVAKIAQFKRECPSIFAWEIRDRLLSEGICTNENIP

SVSSINRVLRNLASGEKNTLQSLQSADPQMLEKLRLLNGNAWPHPGPWPYPPSTAGAPPPQTNGNVTTKK

EGDGKLASQILTLHGYQDQGDGSNDDSDEAQARLRLKRKLQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRRSQDSDSSSPSRIPISSSFSTATMYQPIAPPSAPV

MSRSSHAGLTDSYSSLPPVPSFSVPGNMAPMPSMQQSRDQTSYSCMIPHSTAMTPRGYDSLALGSYNPTH

AGHHVTTTHPSHMQAPSMPGHSHMSHANGGSAGLISPGVSVPVQVPGAVTEEMTSQPYWPRIQ

>gi|21667881|gb|AAM74161.1|AF513712_1 Pax-6 protein [Euprymna scolopes]

MKNTTENHQHSVSHDTNSTSLNSSGASPNEQSPTAWKWSTNPVITEESPRDKPTGHSGVNQLGGVFVNGR

PLPDSTRQRIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVQKIAQ


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Example of foreach/for loop

C shells

bash

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glengoyne% echo $SHELL/bin/tcsh

glengoyne% lsblue1 blue2 blue3 blue4 blue5 blue6 green1 green2 green3 green4

green5 green6glengoyne% foreach colour (blue*)foreach? cp $colour $colour.copyforeach? end

glengoyne% lsblue1 blue2.copy blue4 blue5.copy green1 green4

blue1.copy blue3 blue4.copy blue6 green2 green5

blue2 blue3.copy blue5 blue6.copy green3 green6

gogo$ echo $SHELL/bin/bashgogo$ lsblue1 blue3 blue5 green1

green3 green5 testdir3

blue2 blue4 blue6 green2 green4 green6gogo$ for colour inblue*;do> cp $colour $colour.copy>done

gogo$ lsblue1 blue2.copy blue4 blue5.copy green1 green4

testdir3

blue1.copy blue3 blue4.copy blue6 green2 green5

blue2 blue3.copy blue5 blue6.copy green3 green6


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Next step: scripting

using the shell or a programminglanguage like perl

example: read and make a fasta file froman excel/tab-delimited text probe list

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Simple perl script

#!/usr/bin/perl -w

open (LIST, "illumina_probes_table.txt");

open (SEQ, ">illumina_probes_seq.fasta");

while ($line = ) {

chomp $line;

@fields = split(/\t/,$line);

$id=$fields[1];

$locus{$id}=$fields[0];

$seq{$id}=$fields[9];

print SEQ ">$id $locus{$id}\n$seq{$id}\n\n";

}

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open the input file, create an outputfile and associate them withfilhandles

use perl

for each line in the input file, do thefollowing

Split the line based on a separator(here a tabulation \t) and assign thevalues to a variable called fields.fields[0]=column 1,fields[9]=column10, etc

print the probe id, locus name andsequence in the output file


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Perl script output:

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>106940692

0610005C13RIKTTTGCAGTTCCACCCCTTACCTAGGGTGTGCGGAAGCTG

GGGCGCCCCGT>580022

0610005I04GCTTCTGGATAGGAGAGGGGATATTGTATTGATTCACCCCAT

CTTGTGTC>2940601

0610006I08RIKGACCTCCCTGGCTGTTGCAGCCTTGTCCAGACCTCTGAG

CCGAGTACCTG>103440070

0610006L08RIKGCCCCGCTTCTTCAGCATAACACACGAGCTCTCAGATCT

TCCAATGGAGT>102260551

0610007C21RIKCACCACCTCGGGGGTCTTGTGGACACTTGGTTCAGGAGT

GGACTCGTACT>102370333

0610007C21RIKGCGCACCCTCATCTATCAAGTCCCGGCCATGTCGCAGCC

AAGAAGATTTA


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Bioinformatics common

programs EMBOSS suite

Clustalw

Blast RepeatMasker

Genewise

Etc,


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Sequences format

- different formats, but the most universal one isFASTA

>seq1 other comments if necessarycagtcatgctagctagctagctagctagctagctagtgtggtgtgggggtagctgatcgat

Or

>seq1

CGATGCATGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTGACGTACGTAGCTAGCTGAGCTAGCATGC

>SEQ22

ATCGATCGTAGCTACGACGGTGGGTGATGTCGTAGTTATATAAAATGCTGATGCTAGCTAGCTAGTCGA

E b it


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Emboss suite

Help: online: http://emboss.sourceforge.net/

In Unix:

- wossname + keywordgogo$ wossname alignFinds programs by keywords in their short descriptionSEARCH FOR

'ALIGN'aligncopy Reads and writes alignmentsaligncopypair Reads and writes

pairs from alignmentscons Create a consensus sequence from a multiplealignmentconsambig Create an ambiguous consensus sequence from a multiple

alignmentdiffseq Compare and report features of two similar

sequencesdistmat Create a distance matrix from a multiple sequence

alignmentdotmatcher Draw a threshold dotplot of two sequencesdotpath

Draw a non-overlapping wordmatch dotplot of two sequencesdottup Displays a

wordmatch dotplot of two sequencesedialign Local multiple alignment of

sequencesemma Multiple sequence alignment (ClustalW wrapper)est2genome

Align EST sequences to genomic DNA sequenceextractalign Extract regions from a

sequence alignment
http://emboss.sourceforge.net/docs/http://emboss.sourceforge.net/docs/http://emboss.sourceforge.net/docs/


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Help on a specific program:

Program_name -help -verbose

philippe2-lt:ian_repeat gogo$ seqret -help -verbose Standard (Mandatory) qualifiers:

[-sequence] seqall (Gapped) sequence(s) filename and optional

format, or reference (input USA) [-outseq] seqoutall

[.] Sequence set(s) filename and

optional format (output USA) Additional (Optional) qualifiers: (none) Advanced

(Unprompted) qualifiers: -feature boolean Use feature information -

firstonly boolean [N] Read one sequence and stop Associated qualifiers:"-sequence" associated qualifiers -sbegin1 integer Start of each

sequence to be used -send1 integer End of each sequence to be used

-sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask

for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -

sprotein1 boolean Sequence is protein -slower1 boolean

Make lower case -supper1 boolean Make upper case -sformat1

string Input sequence format -sdbname1 string Database name -

sid1 string Entryname -ufo1 string UFO features

-fformat1 string Features format -fopenfile1 stringFeatures file name "-outseq" associated qualifiers -osformat2 string

Output seq format -osextension2 string File name extension -osname2

string Base file name -osdirectory2 string Output directory


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Emboss Examples:

seqret remap

transeq

revseq


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EMBOSS examples

seqret

glengoyne% more testseq.fasta

>testseq

NNNNNNNNNNNNNNNGNNNNCTCCNTTTNNTCGTTTTTCTTTGAAATTTCTCCCCCCTCCAGTTCGCTGTCCGGCCCTCACAT

TGTGAGAGGGGCAGTGTGCCGTTAATGGCCGTGCCGGGCACCGGGCCGCTCTGGTAGTGCTGGGACATGTGAAGTCTGCTGGG

GCGGCGGGTTCCGGCACCTCGGCGCCGGGGAGATACATGCTGATCATGTCCCGGAGGTCCCCGGCCTGGCAGGGCGCCCTGGATGGGAGGAAGAGGTAACCACAGGGGGGCTGGAGCTGGCCTCGGACTTGACCACCGAACCCATGGAGCCAAGAGCCATGCCAGG

GTGCCCTGCTGCGAGTAGGACATGCTGTAGGTGGGCGAGCCGTTCATGTAGGTCTGCGAGCTGGTCATGGAGTTGTACTGCAG

GCGCTCACGTCGTANCGGTGCATGGGCTGCATCTGCGCTGCGCCGTGCGCATTGAGGCCCGGGTGCTGCGGGTAGCCCAGCTG

TCCTGCATCATGCTGTAGCTGCCGTTGCTCCAGCCGTTCATGTGCGCGTAACTGTCCATGCNNNN

glengoyne% seqret -sbegin 50 -send 100 testseq.fasta testseq_50_100.fasta

Reads and writes (returns) sequences

glengoyne% more testseq_50_100.fasta>testseq

CTCCCCCCTCCAGTTCGCTGTCCGGCCCTCACATGTGTGAGAGGGGCAGTG

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EMBOSS examples


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EMBOSS examples

remap

glengoyne% remap -sbegin 50 -send 1000 testseq.fastaDisplay a sequence with restriction cut sites, translation etc..

Comma separated enzyme list [all]:

Minimum recognition site length [4]: 8

Output file [testseq.remap]:

glengoyne% more testseq.remap

testseq

OliIMslI

\

CTCCCCCCTCCAGTTCGCTGTCCGGCCCTCACATGTGTGAGAGGGGCAGTGTGCCGTTAA

50 60 70 80 90 100

|----:----|----:----|----:----|----:----|----:----|----:----

GAGGGGGGAGGTCAAGCGACAGGCCGGGAGTGTACACACTCTCCCCGTCACACGGCAATT

/

MslI

OliI

P P S S S L S G P H M C E R G S V P L M

L P P P V R C P A L T C V R G A V C R *

S P L Q F A V R P S H V * E G Q C A V N

|----:----|----:----|----:----|----:----|----:----|----:----

E G G E L E S D P G * M H S L P L T G N

E G R W N A T R G E C T H S P C H A T L

R G G G T R Q G A R V H T L P A T H R * 28


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EMBOSS examples

transeqglengoyne% transeq -sbegin 50 -send 100 -frame 3 testseq.fasta

Translate nucleic acid sequences

Output sequence [testseq.pep]:

glengoyne% more testseq.pep

>testseq_3PPSSSLSGPHMCERGS

revseqglengoyne% revseq -sbegin 50 -send 100 testseq.fasta testseq.rev

Reverse and complement a sequence

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l l


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clustalw

Input format: multiple fasta

clustalw seqfilename.fasta

Creates a .aln file

muscle Input format: multiple fasta

muscle -in seqfilename.fasta -

out outputname -clw

Creates a clustal-like output file

Other: T-coffee, dialign, etc


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clustalw

muscle

t_coffee


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Blast - local How to create your own blast database?

- formatdb

- e.g: formatdb -i allseq.fasta -p F

glengoyne% formatdb hformatdb 2.2.11 arguments: -t Title for

database file [String] Optional -i Input file(s) for formatting

[File In] Optional -l Logfile name: [File Out] Optional default

= formatdb.log -p Type of file T - protein F -

nucleotide [T/F] Optional default = T -o Parse options T

- True: Parse SeqId and create indexes. F - False: Do notparse SeqId. Do not create indexes. [T/F] Optional default = F


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Blast - local

blastall

compulsory parameters:-p blastn/blastp/tblastn/blastx/tblastx

-d database

-i input file

-o output file

optional parameters:-e Expectation value (E) [Real] default = 10.0

-m alignment view options:

0 = pairwise,8 = tabular,

9 = tabular with comment lines

e.g: blastall -p blastn -d allseq.fasta -i mycandidate.fasta -o blastoutput.txt


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RepeatMasker

RepeatMasker seq.fasta

RepeatMasker -species mouse seq.fasta

Output:seq.fasta.masked (N where repeat)

seq.fasta.out:SW perc perc perc query position in query matching repeat position in repeatscore div.

del. ins. sequence begin end (left) repeat class/family begin end (left) ID 226 15.8 7.3 11.

Chromosome 38 119 (389882) C MLT1L LTR/MaLR (4) 611 533 1 376 6.7 21.7 0.0Chromosome 200 259 (389742) C MADE1 DNA/Mariner (7) 73 1 2 416 23.4 8.4 8.4

Chromosome 310 536 (389465) C MLT1L LTR/MaLR (348) 267 41 1 268 17.7 0.0 3.4

Chromosome 545 797 (389204) + AluJo SINE/Alu 6 302 (0) 4 2118 12.8 1.6 0.3

Chromosome 882 1187 (388814) + AluSg SINE/Alu 1 310 (0) 6 309 28.3 5.9 7.7

Chromosome 1202 1487 (388514) + L1ME4a LINE/L1 5841 6121 (0) 7 2047 22.2 11.0 4.2

Chromosome 1659 1837 (388164) + MLT1G LTR/MaLR 10 175 (415) 8 2002 13.1 0.3 0.3

Chromosome 1838 2127 (387874) C AluSx SINE/Alu (22) 290 1 9 2047 22.2 11.0 4.2

Chromosome 2128 2491 (387510) + MLT1G LTR/MaLR 175 590 (0) 8 208 21.4 0.0 0.0

Chromosome 2853 2894 (387107) + MIR SINE/MIR 70 111 (151) 10 218 6.9 0.0 6.9

Chromosome 3083 3140 (386861) + (TA)n Simple_repeat 1 54 (0) 11


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R package

open source scripting platform forstatistical computing

versions for Windows, OS X, Linux.

Graphical interface, terminal andprogrammatic interfaces

wealth of documentation onlineas well as local support

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R k


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R package

36


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collection of packages providing tools forthe analysis and comprehension of genomic data

great many algorithms/ techniques peer-reviewed(5,670 Google Scholar hits)

developed in response to large data volumesand non-trivial analysis involvedwith microarrays

http://www.bioconductor.org

number of packages within the bioconductor project by year
http://www.bioconductor.org/http://www.bioconductor.org/http://www.bioconductor.org/


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Selection of packages:

package description

biomaRt interface to BioMart databases (incl. Ensembl)

affy methods for analysing Affymetric oligonucleotide microarrays

ShortRead methods for analysing high-throughput short-read sequencingdata (incl. Solexa)

ppiStats protein-protein interaction statistical methods

beadarray quality assessment and low-level analysis of Illumina BeadArrays

fbat family-based association tests for genetic data

limma linear models for detecting differential expression in microarray data

See introduction course in January,contact Vicky Sabine for moreinformation
mailto:[email protected]:[email protected]

Documents

Introductory Unix