10 More Discussions You Might Find Interesting
1. UNIX for Beginners Questions & Answers
Hello!
I need some advices from You. How many days i need to setup cluster using virtual box for mid exp user? Do you have any ideas related to master thesis related to clustering? I need to include some search aspect within that topic.Can You recommend some books/docs about that case?
Thank... (4 Replies)
Discussion started by: protos27
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2. Ubuntu
Hi All,
I am new user here and a new one to try clustering with Ubuntu nodes, and need help. If I should be in another place please mention.
I have a two nodes with Ubuntu 14.04 installed on them. I need to make a cluster consisting of these two nodes with purpose of experimentation with... (3 Replies)
Discussion started by: IncognitoExpert
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3. HP-UX
Hello guys,
I would like to ask for your assistance, since i am new to HP-UX.
Please give me some documentation about clustering in HP-UX. More precisely design,architecture, configuring etc. I am working on my master thesis right now and would like to include some guidance about that.... (1 Reply)
Discussion started by: bazillion
1 Replies
4. Red Hat
Hello,
I'm new in this forum.
I'll have a new project to change architecture for our servers.
From one server where we found database oracle 9i and Oracle application ebs 11 installed in HPux to cluster that contain nodes in redhat.
Can you give me a detailed documentation that... (1 Reply)
Discussion started by: Safi1982
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5. Linux
Hi,
I have done the OS clustering in linux redhat 5.6, my one node is down and when i am trying to reboot the other node it is not coming up. any pointer to this would be helpful.
the SAN storage luns are not coming as mounted (2 Replies)
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6. UNIX for Dummies Questions & Answers
hi guys
Some time ago I used Linux HA(Heartbeat) to setup like 3 cluster.
Now I have to install another 2 cluster and was checking more info to be sure HA was still used but I found some other stuff like OpenAIS - Corosync - Pacemaker to tell you the truth I am kinda confused here
I get... (0 Replies)
Discussion started by: karlochacon
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7. Solaris
SunOS 5.10 Generic_142900-15 sun4u sparc SUNW,SPARC-Enterprise
How can I tell if "clustering" is being used in my shop?
I have to file systems that are identical. These filesystems are nfs mounted. But how can I tell if they are being kept in sync as a result of clustering or some other... (2 Replies)
Discussion started by: Harleyrci
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8. HP-UX
hi,
do u know any link that will get back to me up to speed on hp serviceguard on clustering?
thanks and much appreciated,
itik (2 Replies)
Discussion started by: itik
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9. UNIX for Advanced & Expert Users
Can anybody help me how to mirror the solaris 10 step-by-step with veritas. Have two disks. Then how can I cluster with veritas (1 Reply)
Discussion started by: karole
1 Replies
10. IP Networking
Can someone please help me to cluster two SUN Ultra 5 Boxes to run a application ? I am running Solaris 7 with two Ethernet NICs in each box. The Primary nics have a address of 10.10.10.24x and the other two nics have a multicast address of 224.0.1.27 each. I want to run a application at work... (6 Replies)
Discussion started by: keyur
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PSI-CD-HIT-2D.PL(1) User Commands PSI-CD-HIT-2D.PL(1)
NAME
psi-cd-hit-2d.pl - runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format
DESCRIPTION
Usage psi-cd-hit-2d [Options]
Options
-i in_dbname, required
-o out_dbname, required
-c clustering threshold (sequence identity), default 0.3
-ce clustering threshold (blast expect), default -1,
it means by default it doesn't use expect threshold, but with positive value, the program cluster seqs if similarities meet either
identity threshold or expect threshold
-L coverage of shorter sequence ( aligned / full), default 0.0
-M coverage of longer sequence ( aligned / full), default 0.0
-R (1/0) use psi-blast profile? default 0 perform psi-blast / pdb-blast type search
-G (1/0) use global identity? default 1 sequence identity calculated as
total identical residues of local alignments / length of shorter seq
if you prefer to use -G 0, it is suggested that you also use -L, such as -L 0.8, to prevent very short matches.
-d length of description line in the .clstr file, default 30 if set to 0, it takes the fasta defline and stops at first space
-l length_of_throw_away_sequences, default 10
-p profile search para, default
"-a 2 -d nr80 -j 3 -F F -e 0.001 -b 500 -v 500"
-bfdb profile database, default nr80
-s blast search para, default
"-F F -e 0.000001 -b 100000 -v 100000"
-be blast expect cutoff, default 0.000001
-b filename of list of hosts to run this program in parallel with ssh calls, you need provide a list of hosts
-pbs No of jobs to send each time by PBS querying system
you can not use both ssh and pbs at same time
-k (1/0) keep blast raw output file, default 1
-rs steps of save restart file and clustering output, default 5000
everytime after process 5000 sequences, program write a restart file and current clustering information
-restart restart file, readin a restart file
if program crash, stoped, termitated, you can restart it by add a option "-restart sth.restart"
-rf steps of re format blast database, default 200,000
if program clustered 200,000 seqs, it remove them from seq pool, and re format blast db to save time
-local dir of local blast db,
when run in parallel with ssh (not pbs), I can copy blast dbs to local drives on each node to save blast db reading time BUT, IT MAY
NOT FASTER
-J job, job_file, exe specific jobs like parse blast outonly DON'T use it, it is only used by this program itself
-single files of ids those you known that they are singletons
so I won't run them as queries
-i2 second input database
-blastn run blastn, default 0
-lo how long can seq in db2 > db1 in a cluster, default 0
means, that seq in db2 should <= seqs in db1 in a cluster
============================== by Weizhong Li, liwz@sdsc.edu ==============================
If you find cd-hit useful, please kindly cite:
"Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam
GodzikBioinformatics, (2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide
sequences", Weizhong Li & Adam Godzik Bioinformatics, (2006) 22:1658-1659
psi-cd-hit-2d.pl 4.6-2012-04-25 April 2012 PSI-CD-HIT-2D.PL(1)