PfamDB-Sapelo2 - Revision history

Keeko at 18:39, 13 October 2021

2021-10-13T18:39:27Z

← Older revision		Revision as of 14:39, 13 October 2021
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	A database for [[Hmmer]] and [[Pfam_scan]] program		A database for [[Hmmer]] and [[Pfam_scan]] program

	The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).		The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). In some releases Pfam includes both Pfam-A and Pfam-B. Because the entries in Pfam-A do not cover all known proteins, a supplement was provided called Pfam-B. Although of lower quality, Pfam-B families could be useful when no Pfam-A families were found. Pfam-B has been discontinued and reintroduced in various releases.

	More information about Pfam can be found at the [http://pfam.xfam.org/ ~~pfam~~ website]		More information about Pfam can be found at the [http://pfam.xfam.org/ Pfam website]

	There are multiple versions under /db/pfam		There are multiple versions under /db/pfam
	The ~~pfam~~ database must be formatted to work with certain software such as HMMER or Pfam_scan. The non-formulated downloads are numbered with the version of the ~~pfam~~ database.The currently available versions are 27.0 33.0 and 34.0. The versions which have been formatted to work with HMMER are listed with the ~~pfam~~ version followed by the HMMER version they have been formatted for. The currently available versions are 27.0-hmmer3.0 and 34.0-hmmer3.3.2.		The Pfam database must be formatted to work with certain software such as HMMER or Pfam_scan. The non-formulated downloads are numbered with the version of the Pfam database.The currently available versions are 27.0 33.0 and 34.0. The versions which have been formatted to work with HMMER are listed with the Pfam version followed by the HMMER version they have been formatted for. The currently available versions are 27.0-hmmer3.0 and 34.0-hmmer3.3.2.

	<pre class="gscript">		<pre class="gscript">
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	</pre>		</pre>

	The commands to generate the data is documented at UGA file sitting at the same directory with data:		The commands to generate the data is documented at the UGA file sitting at the same directory with data:
	<pre class="gcommand">		<pre class="gcommand">
	formatdb -i Pfam-A.fasta -n Pfam-A -t Pfam-A -l Pfam-A.log -p T		formatdb -i Pfam-A.fasta -n Pfam-A -t Pfam-A -l Pfam-A.log -p T
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	</pre>		</pre>

	If you would like a particular version of the ~~pfam~~ database to work with a particular version of HMMER you can download or prepare this database yourself. To format ~~pfam~~ for use with HMMER you can use the function, hmmpress, which comes built into HMMER. The hmmpress step is required for hmmscan to work.		If you would like a particular version of the Pfam database to work with a particular version of HMMER you can download or prepare this database yourself. To format Pfam for use with HMMER you can use the function, hmmpress, which comes built into HMMER. The hmmpress step is required for hmmscan to work. The following commands can be used to prepare pfam.hmm data.
	The following commands can be used to prepare pfam.hmm data.

	<pre class="gcommand">		<pre class="gcommand">
	ml HMMER/3.1b2-foss-2016b #use whichever version of HMMER you would like to use for hmmscan		ml HMMER/3.1b2-foss-2016b #use whichever version of HMMER you would like to use for hmmscan
			wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz #wget which ever version of Pfam you would like
			gunzip Pfam-A.hmm.gz
	hmmpress Pfam-A.hmm		hmmpress Pfam-A.hmm
	~~hmmpress Pfam-B.hmm~~
	</pre>		</pre>

Keeko at 18:07, 13 October 2021

2021-10-13T18:07:43Z

← Older revision		Revision as of 14:07, 13 October 2021
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]
	A database for [[Hmmer]] and [[Pfam_scan]] program		A database for [[Hmmer]] and [[Pfam_scan]] program

			The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

			More information about Pfam can be found at the [http://pfam.xfam.org/ pfam website]

	There are multiple versions under /db/pfam		There are multiple versions under /db/pfam
	The pfam database must be formatted to work with certain software such as HMMER. The non-formulated downloads are numbered with the version of the pfam database.The currently available versions are 27.0 33.0 and 34.0. The versions which have been formatted to work with HMMER are listed with the pfam version followed by the HMMER version they have been formatted for. The currently available versions are 27.0-hmmer3.0 and 34.0-hmmer3.3.2.		The pfam database must be formatted to work with certain software such as HMMER or Pfam_scan. The non-formulated downloads are numbered with the version of the pfam database.The currently available versions are 27.0 33.0 and 34.0. The versions which have been formatted to work with HMMER are listed with the pfam version followed by the HMMER version they have been formatted for. The currently available versions are 27.0-hmmer3.0 and 34.0-hmmer3.3.2.

	<pre class="gscript">		<pre class="gscript">
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	</pre>		</pre>

	Databases are download install files from [~~ftp~~://ftp.sanger.ac.uk/pub/databases/Pfam/releases~~/Pfam27.0~~/ sanger] website.		Databases are download install files from [http://bio.nic.funet.fi/pub/mirrors/ftp.sanger.ac.uk/pub/databases/Pfam/releases/ sanger] website.

Keeko at 17:58, 13 October 2021

2021-10-13T17:58:20Z

← Older revision		Revision as of 13:58, 13 October 2021
Line 3:		Line 3:

	There are multiple versions under /db/pfam		There are multiple versions under /db/pfam
			The pfam database must be formatted to work with certain software such as HMMER. The non-formulated downloads are numbered with the version of the pfam database.The currently available versions are 27.0 33.0 and 34.0. The versions which have been formatted to work with HMMER are listed with the pfam version followed by the HMMER version they have been formatted for. The currently available versions are 27.0-hmmer3.0 and 34.0-hmmer3.3.2.

	<pre class="gscript">		<pre class="gscript">
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	</pre>		</pre>

	The ~~command generated~~ the data is documented at UGA file sitting at the same directory with data:		The commands to generate the data is documented at UGA file sitting at the same directory with data:
	<pre class="gcommand">		<pre class="gcommand">
	formatdb -i Pfam-A.fasta -n Pfam-A -t Pfam-A -l Pfam-A.log -p T		formatdb -i Pfam-A.fasta -n Pfam-A -t Pfam-A -l Pfam-A.log -p T
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	xdformat -p -x Pfam-A.fasta		xdformat -p -x Pfam-A.fasta
	xdformat -p Pfam-B.fasta		xdformat -p Pfam-B.fasta
			</pre>

			If you would like a particular version of the pfam database to work with a particular version of HMMER you can download or prepare this database yourself. To format pfam for use with HMMER you can use the function, hmmpress, which comes built into HMMER. The hmmpress step is required for hmmscan to work.
			The following commands can be used to prepare pfam.hmm data.

			<pre class="gcommand">
			ml HMMER/3.1b2-foss-2016b #use whichever version of HMMER you would like to use for hmmscan
			hmmpress Pfam-A.hmm
			hmmpress Pfam-B.hmm
	</pre>		</pre>

Yhuang: Created page with "Category:Sapelo2Category:SoftwareCategory:BioinformaticsCategory:Bioinformatics Database A database for Hmmer and Pfam_scan program There are mult..."

2018-06-28T14:26:35Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics Category:Bioinformatics Database A database for Hmmer and Pfam_scan program There are mult..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]
A database for [[Hmmer]] and [[Pfam_scan]] program

There are multiple versions under /db/pfam

<pre class="gscript">
/db/pfam/
</pre>

The command generated the data is documented at UGA file sitting at the same directory with data:
<pre class="gcommand">
formatdb -i Pfam-A.fasta -n Pfam-A -t Pfam-A -l Pfam-A.log -p T
formatdb -i Pfam-B.fasta -n Pfam-A -t Pfam-A -l Pfam-A.log -p T
ml HMMER/3.1b2-foss-2016b
hmmpress Pfam-A.hmm
hmmpress Pfam-B.hmm
ml WU-Blast/2.2.6-foss-2016b
xdformat -p -x Pfam-A.fasta
xdformat -p Pfam-B.fasta
</pre>

version built with hmmer 3.0 ([[Pfam_scan]] friendly)

<pre class="gscript">
/db/pfam/27.0-hmmer3.0/Pfam-A
/db/pfam/27.0-hmmer3.0/Pfam-B
/db/pfam/27.0-hmmer3.0/Pfam-A.hmm
/db/pfam/27.0-hmmer3.0/Pfam-B.hmm
</pre>

Databases are download install files from [ftp://ftp.sanger.ac.uk/pub/databases/Pfam/releases/Pfam27.0/ sanger] website.