Biol425 2019 - Revision history

imported>Ntino at 19:40, 6 February 2020

2020-02-06T19:40:46Z

← Older revision		Revision as of 19:40, 6 February 2020
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	## Extract sequences into a FASTA file: <code>../../bio425/bin/extract ../../bio425/data/GBB.1con-splitted/Borrelia_burgdorferi_4041_cp9_plasmid_C.fas cp9.coord2 > cp9.fas</code> [Note two input files and standard output, which is then redirected (i.e., saved) into a new file]		## Extract sequences into a FASTA file: <code>../../bio425/bin/extract ../../bio425/data/GBB.1con-splitted/Borrelia_burgdorferi_4041_cp9_plasmid_C.fas cp9.coord2 > cp9.fas</code> [Note two input files and standard output, which is then redirected (i.e., saved) into a new file]
	# bioseq		# bioseq
	## Add <code>bp-utils</code> into $PATH by export PATH=$PATH:../../bio425/bp-utils:../../bio425/bin/		## Add <code>bp-utils</code> into $PATH by export PATH=$PATH:$HOME/../../bio425/bp-utils:../../bio425/bin/
	## Run <code>bioseq</code> with these options: <code>-l, -n, -c, -r, -t1, -t, -t6, and -s</code>		## Run <code>bioseq</code> with these options: <code>-l, -n, -c, -r, -t1, -t, -t6, and -s</code>
	## In-Class Challenge: use <code>bioseq</code> to extract and translate the 1st (+1 frame) and 5th (-1 frame) genes.		## In-Class Challenge: use <code>bioseq</code> to extract and translate the 1st (+1 frame) and 5th (-1 frame) genes.
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	# Using ssh, log into eniac.cs.hunter.cuny.edu & then ssh into another host (e.g. "cslab8") for the exercises - REQUIRED IF YOU ARE WORKING REMOTELY!		# Using ssh, log into eniac.cs.hunter.cuny.edu & then ssh into another host (e.g. "cslab8") for the exercises - REQUIRED IF YOU ARE WORKING REMOTELY!
	# Copy data file <code>../../bio425/data/mystery_seq1.fas</code> into your home directry		# Copy data file <code>../../bio425/data/mystery_seq1.fas</code> into your home directry
	# Add <code>/data/biocs/b/bio425/bin</code> to your the $PATH export PATH=$PATH:../../bio425/bp-utils:../../bio425/bin/		# Add <code>/data/biocs/b/bio425/bin</code> to your the $PATH export PATH=$PATH:$HOME/../../bio425/bp-utils:../../bio425/bin/
	# Use the <code>long-orf</code> command to predict ORFs on the mystery_seq1. Save resulting coord file as "mystery_seq1.coord".		# Use the <code>long-orf</code> command to predict ORFs on the mystery_seq1. Save resulting coord file as "mystery_seq1.coord".
	# Extract ONLY the lines containing ORF information into a new file "mystery_seq1.coord2" using <code>grep</code>		# Extract ONLY the lines containing ORF information into a new file "mystery_seq1.coord2" using <code>grep</code>

imported>Ntino at 19:39, 6 February 2020

2020-02-06T19:39:25Z

← Older revision		Revision as of 19:39, 6 February 2020
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	# bioseq		# bioseq
	## Add <code>bp-utils</code> into $PATH by export PATH=$PATH:../../bio425/bp-utils:../../bio425/bin/		## Add <code>bp-utils</code> into $PATH by export PATH=$PATH:../../bio425/bp-utils:../../bio425/bin/

	~~</code>~~
	## Run <code>bioseq</code> with these options: <code>-l, -n, -c, -r, -t1, -t, -t6, and -s</code>		## Run <code>bioseq</code> with these options: <code>-l, -n, -c, -r, -t1, -t, -t6, and -s</code>
	## In-Class Challenge: use <code>bioseq</code> to extract and translate the 1st (+1 frame) and 5th (-1 frame) genes.		## In-Class Challenge: use <code>bioseq</code> to extract and translate the 1st (+1 frame) and 5th (-1 frame) genes.

imported>Ntino at 19:38, 6 February 2020

2020-02-06T19:38:51Z

imported>Ntino at 18:58, 30 January 2020

2020-01-30T18:58:57Z

← Older revision		Revision as of 18:58, 30 January 2020
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	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"
	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #1 - (<font color="red">Due Wednesday 2/07/~~2018~~, at 10am - Submit Responses on Blackboard as document with all command line outputs</font>)		! Assignment #1 - (<font color="red">Due Wednesday 2/05/2020, at 10am - Submit Responses on Blackboard as document with all command line outputs</font>)
	\|- style="background-color:powderblue;"		\|- style="background-color:powderblue;"
	\| '''Unix Text Filters''' (10 pts) Show both commands and outputs for the following questions:<br>		\| '''Unix Text Filters''' (10 pts) Show both commands and outputs for the following questions:<br>

imported>Ntino at 19:22, 3 April 2019

2019-04-03T19:22:23Z

← Older revision		Revision as of 19:22, 3 April 2019
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	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"
	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #8 (<font color="red">Due Wednesday 4/24/2019, at 10am - Submit Responses on Blackboard</font>)		! Assignment #8 (<font color="red">Due Wednesday 5/1/2019, at 10am - Submit Responses on Blackboard</font>)
	\|- style="background-color:powderblue;"		\|- style="background-color:powderblue;"
	\|		\|

imported>Ntino at 19:21, 3 April 2019

2019-04-03T19:21:44Z

← Older revision		Revision as of 19:21, 3 April 2019
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	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"
	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #7 (<font color="red">Due 4/24/2019, at 10am - Submit Responses on Blackboard</font>)		! Assignment #7 (<font color="red">Due 4/17/2019, at 10am - Submit Responses on Blackboard</font>)
	\|- style="background-color:powderblue;"		\|- style="background-color:powderblue;"
	\|		\|

imported>Ntino at 19:19, 3 April 2019

2019-04-03T19:19:48Z

← Older revision		Revision as of 19:19, 3 April 2019
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	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"
	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"
	! Assignment #7 (<font color="red">Due 4/17/2019, at 10am - Submit Responses on Blackboard</font>)		! Assignment #7 (<font color="red">Due 4/24/2019, at 10am - Submit Responses on Blackboard</font>)
	\|- style="background-color:powderblue;"		\|- style="background-color:powderblue;"
	\|		\|

imported>Ntino at 12:36, 3 April 2019

2019-04-03T12:36:11Z

@@ Line 647: / Line 647: @@
 * [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']
-FINAL WILL POSTED HERE AND WILL BE DUE Wednesday 5/16/2018.
+* Review slides: [[File:Review-Session.pdf|thumbnail]]
 ===Wednesday, May 15 at 10am - FINAL EXAM DUE - UPLOAD ON BLACKBOARD ===

imported>Ntino at 12:33, 3 April 2019

2019-04-03T12:33:38Z

← Older revision		Revision as of 12:33, 3 April 2019
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	\|}		\|}

	===May 8: Q&A on everything covered in the course - material review before FINAL ===		===May 1: Q&A on everything covered in the course - material review before FINAL ===

	* PLEASE FILL IN TEACHER EVALUATIONS: [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']		* PLEASE FILL IN TEACHER EVALUATIONS: [http://www.hunter.cuny.edu/te '''Teacher's evaluation''']

imported>Ntino at 12:32, 3 April 2019

2019-04-03T12:32:51Z

← Older revision		Revision as of 12:32, 3 April 2019
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	\|}		\|}

	=== April ~~24 and May 1~~ Regular Expressions===		=== April 17 Regular Expressions===
	* Learning goals: Perl Regular Expressions and Pattern Matching		* Learning goals: Perl Regular Expressions and Pattern Matching
	* Lecture slides: [http://diverge.hunter.cuny.edu/w/images/2/24/4-13-16-Lecture-Slides.pdf Lecture Slides]		* Lecture slides: [http://diverge.hunter.cuny.edu/w/images/2/24/4-13-16-Lecture-Slides.pdf Lecture Slides]

← Older revision		Revision as of 19:38, 6 February 2020
Line 78:		Line 78:
	## Extract sequences into a FASTA file: <code>../../bio425/bin/extract ../../bio425/data/GBB.1con-splitted/Borrelia_burgdorferi_4041_cp9_plasmid_C.fas cp9.coord2 > cp9.fas</code> [Note two input files and standard output, which is then redirected (i.e., saved) into a new file]		## Extract sequences into a FASTA file: <code>../../bio425/bin/extract ../../bio425/data/GBB.1con-splitted/Borrelia_burgdorferi_4041_cp9_plasmid_C.fas cp9.coord2 > cp9.fas</code> [Note two input files and standard output, which is then redirected (i.e., saved) into a new file]
	# bioseq		# bioseq
	## Add <code>bp-utils</code> into $PATH by ~~editing the~~ .~~bash_profile file and run <code>source~~ .~~bash_profile~~</code>		## Add <code>bp-utils</code> into $PATH by export PATH=$PATH:../../bio425/bp-utils:../../bio425/bin/

			</code>
	## Run <code>bioseq</code> with these options: <code>-l, -n, -c, -r, -t1, -t, -t6, and -s</code>		## Run <code>bioseq</code> with these options: <code>-l, -n, -c, -r, -t1, -t, -t6, and -s</code>
	## In-Class Challenge: use <code>bioseq</code> to extract and translate the 1st (+1 frame) and 5th (-1 frame) genes.		## In-Class Challenge: use <code>bioseq</code> to extract and translate the 1st (+1 frame) and 5th (-1 frame) genes.
Line 102:		Line 104:
	# Using ssh, log into eniac.cs.hunter.cuny.edu & then ssh into another host (e.g. "cslab8") for the exercises - REQUIRED IF YOU ARE WORKING REMOTELY!		# Using ssh, log into eniac.cs.hunter.cuny.edu & then ssh into another host (e.g. "cslab8") for the exercises - REQUIRED IF YOU ARE WORKING REMOTELY!
	# Copy data file <code>../../bio425/data/mystery_seq1.fas</code> into your home directry		# Copy data file <code>../../bio425/data/mystery_seq1.fas</code> into your home directry
	# Add <code>/data/biocs/b/bio425/bin</code> to your the $PATH ~~variable in the "~~.~~bash_profile" file (using vi or emacs)~~.		# Add <code>/data/biocs/b/bio425/bin</code> to your the $PATH export PATH=$PATH:../../bio425/bp-utils:../../bio425/bin/
	~~# Run <code>source ~~~/.~~bash_profile<~~/~~code> to activate the above path~~
	# Use the <code>long-orf</code> command to predict ORFs on the mystery_seq1. Save resulting coord file as "mystery_seq1.coord".		# Use the <code>long-orf</code> command to predict ORFs on the mystery_seq1. Save resulting coord file as "mystery_seq1.coord".
	# Extract ONLY the lines containing ORF information into a new file "mystery_seq1.coord2" using <code>grep</code>		# Extract ONLY the lines containing ORF information into a new file "mystery_seq1.coord2" using <code>grep</code>