Recent changes to findprimer.py

WikiPage findprimer.py modified by Sarah Bourlat

Sarah Bourlat — Tue, 24 Jul 2012 10:32:11 -0000

--- v5
+++ v6
@@ -2,9 +2,9 @@
 
 Primer trimming: 
 
-To find and remove primer binding sites and upstream sequences we have written the python script findprimer.py. Due to vector cloning our sequences can be in either 3’-5’ or 5’-3’ orientation.
+To find and remove primer binding sites and upstream sequences we have written the python script findprimer.py. Due to vector cloning our sequences can be in either 3’-5’ or 5’-3’ orientation, and the script takes this into account by reversing the sequences.
 
-This script searches for the forward primer (in our case Lco1490) and reverses the sequences where the forward primer is not found. The sequences are then searched again and trimmed upstream and including the forward primer. See attachment for a figure on how the code works.
+This script searches for the forward primer (in our case Lco1490) and reverses the sequences where the forward primer is not found. The sequences are then searched again and trimmed upstream and including the forward primer. See the attachment for a figure on how the code works.
 
 The full length of the primer is 25 bp and we have found that searching with only the last 7bp of the primer maximises the chances of finding the primer in the sequence. Reducing the primer length further is not desirable as it increases the chance of randomly finding the sequence in the middle of the cytochrome oxidase 1 gene.

WikiPage findprimer.py modified by Sarah Bourlat

Sarah Bourlat — Mon, 23 Jul 2012 13:49:12 -0000

--- v4
+++ v5
@@ -1,4 +1,6 @@
-findprimer.py (Primer trimming): 
+[findprimer.py](https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/findprimer.py) 
+
+Primer trimming: 
 
 To find and remove primer binding sites and upstream sequences we have written the python script findprimer.py. Due to vector cloning our sequences can be in either 3’-5’ or 5’-3’ orientation.

WikiPage findprimer.py modified by MV2012

MV2012 — Fri, 20 Jul 2012 09:25:57 -0000

--- v3
+++ v4
@@ -1,8 +1,8 @@
-findprimer.py (Primer trimming) Figure 2: 
+findprimer.py (Primer trimming): 
 
 To find and remove primer binding sites and upstream sequences we have written the python script findprimer.py. Due to vector cloning our sequences can be in either 3’-5’ or 5’-3’ orientation.
 
-This script searches for the forward primer (in our case Lco1490) and reverses the sequences where the forward primer is not found. The sequences are then searched again and trimmed upstream and including the forward primer. 
+This script searches for the forward primer (in our case Lco1490) and reverses the sequences where the forward primer is not found. The sequences are then searched again and trimmed upstream and including the forward primer. See attachment for a figure on how the code works.
 
 The full length of the primer is 25 bp and we have found that searching with only the last 7bp of the primer maximises the chances of finding the primer in the sequence. Reducing the primer length further is not desirable as it increases the chance of randomly finding the sequence in the middle of the cytochrome oxidase 1 gene.

WikiPage findprimer.py modified by MV2012

MV2012 — Fri, 20 Jul 2012 09:25:20 -0000

--- v2
+++ v3
@@ -1,3 +1,15 @@
 findprimer.py (Primer trimming) Figure 2: 
 
-To find and remove primer binding sites and upstream sequences we have written the python script findprimer.py. This script searches for the forward primer (in our case Lco1490) and reverses the sequences where the forward primer is not found. Due to vector cloning our sequences can be in either 3’-5’ or 5’-3’ orientation. The sequences are then searched again and trimmed upstream and including the forward primer. The full length of the primer is 25 bp and we have found that searching with only the last 7bp of the primer maximises the chances of finding the primer in the sequence. Reducing the primer length further is not desirable as it increases the chance of randomly finding the sequence in the middle of the cytochrome oxidase 1 gene. The 5’ trimmed sequences are then searched for the reverse primer (Hco2198) and trimmed including all downstream sequences. The output includes a count of the number of sequences in the input file, the number of sequences in forward orientation, the number of sequences reversed, the number of sequences trimmed  upstream and including the forward primer and the number of sequences trimmed downstream and including the reverse primer. This allows the whole process to be monitored on the terminal window. Three output files are generated: One with all the sequences in forward orientation, one with all the sequences after trimming for the forward primer, and one with all the sequences after trimming for the reverse primer. Each output file will be used in the script as an input file in the following step, such as sequences in the last output file will be in forward orientation with both primers trimmed. After primer trimming, size filtering of the sequences was done to remove those sequences that are <200bp, using the python script filtering.py.
+To find and remove primer binding sites and upstream sequences we have written the python script findprimer.py. Due to vector cloning our sequences can be in either 3’-5’ or 5’-3’ orientation.
+
+This script searches for the forward primer (in our case Lco1490) and reverses the sequences where the forward primer is not found. The sequences are then searched again and trimmed upstream and including the forward primer. 
+
+The full length of the primer is 25 bp and we have found that searching with only the last 7bp of the primer maximises the chances of finding the primer in the sequence. Reducing the primer length further is not desirable as it increases the chance of randomly finding the sequence in the middle of the cytochrome oxidase 1 gene. 
+
+The 5’ trimmed sequences are then searched for the reverse primer (Hco2198) and trimmed including all downstream sequences. 
+
+The output includes a count of the number of sequences in the input file, the number of sequences in forward orientation, the number of sequences reversed, the number of sequences trimmed  upstream and including the forward primer and the number of sequences trimmed downstream and including the reverse primer. This allows the whole process to be monitored on the terminal window. 
+
+Three output files are generated: One with all the sequences in forward orientation, one with all the sequences after trimming for the forward primer, and one with all the sequences after trimming for the reverse primer. Each output file will be used in the script as an input file in the following step, such as sequences in the last output file will be in forward orientation with both primers trimmed. 
+
+

WikiPage findprimer.py modified by SBMV

SBMV — Fri, 20 Jul 2012 08:53:48 -0000

WikiPage findprimer.py modified by SBMV

SBMV — Fri, 20 Jul 2012 08:44:40 -0000

findprimer.py (Primer trimming) Figure 2: To find and remove primer binding sites and upstream sequences we have written the python script findprimer.py. This script searches for the forward primer (in our case Lco1490) and reverses the sequences where the forward primer is not found. Due to vector cloning our sequences can be in either 3’-5’ or 5’-3’ orientation. The sequences are then searched again and trimmed upstream and including the forward primer. The full length of the primer is 25 bp and we have found that searching with only the last 7bp of the primer maximises the chances of finding the primer in the sequence. Reducing the primer length further is not desirable as it increases the chance of randomly finding the sequence in the middle of the cytochrome oxidase 1 gene. The 5’ trimmed sequences are then searched for the reverse primer (Hco2198) and trimmed including all downstream sequences. The output includes a count of the number of sequences in the input file, the number of sequences in forward orientation, the number of sequences reversed, the number of sequences trimmed upstream and including the forward primer and the number of sequences trimmed downstream and including the reverse primer. This allows the whole process to be monitored on the terminal window. Three output files are generated: One with all the sequences in forward orientation, one with all the sequences after trimming for the forward primer, and one with all the sequences after trimming for the reverse primer. Each output file will be used in the script as an input file in the following step, such as sequences in the last output file will be in forward orientation with both primers trimmed. After primer trimming, size filtering of the sequences was done to remove those sequences that are <200bp, using the python script filtering.py.