Actually both the columns of file-B are interacting-protein-partners.
I want to match the column4 of file-A with both the columns of file-B, to see which of the protein of column4, file-A is also present in any of the column of file-B along with its corresponding protein partner.
i.e all columns of file-A + the matching LINE (both columns) of file-B (if either column contains a value same as that in column4 of file-A).
In the given output note that column2 of file-B had the same value as that of column4 file-A.
Dear all,
I have two files in UNIX File1 and File2 as below:
File1:
1,1234,.,67.897,,0
1,4134,.,87.97,,4
0,1564,.,97.8,,1
File2:
2,8798,.,67.897,,0
2,8879,.,77.97,,4
0,1564,.,97.8,,1
I want to do the following:
(1) Make sure that both the files have equal number of columns and if... (1 Reply)
Dear all,
I have two files in UNIX File1 and File2 as below:
File1:
1,1234,.,67.897,,0
1,4134,.,87.97,,4
0,1564,.,97.8,,1
File2:
2,8798,.,67.897,,0
2,8879,.,77.97,,4
0,1564,.,97.8,,1
I want to do the following:
(1) Make sure that both the files have equal number of columns and if... (4 Replies)
I have two files file1 and file 2
both are having multiple coloumns.i want to select only two columns.
i used following code to get the desired columns,with ',' as delimiter
cut -d ',' -f 1,2 file1 | sort > file1.new
cut -d ',' -f 1,2 file2 | sort > file2.new
I want to get the coloums... (1 Reply)
Hey,
I have 2 files that have a name and then a number:
File 1:
dog 21
dog 24
cat 33
cat 27
dog 76
cat 65
File 2:
dog 109
dog 248
cat 323
cat 207
cat 66 (2 Replies)
Hi,
I have two files with the same number of columns. Basically I want to print the 2 columns that match between the two files.
File1 looks like this:
dr12 12 6 abn
dr14 12 7 abn
File2 looks something like this:
dr12 12 8 abn
dr12 14 7 abn
So basically if the first... (1 Reply)
Hi,
I have two files. File1.txt has 2 columns and looks like:
458739 122345
4456 122657
34200 122600
File2.txt has many columns with column 1 the same as column2 of File1.txt, but with lot more rows:
122786 abcdefg user1@email
122778 uuhjeufh user2@email... (1 Reply)
Hello,
I have two files as 1.txt and 2.txt with number as columns.
1.txt
0 53.7988
1 -30.0859
2 20.1632
3 14.2135
4 14.6366
5 -37.6258
.
.
.
31608 -8.57333
31609 -2.58554
31610 -24.2857
2.txt (1 Reply)
Hi,
I have a single-column file1 having records like:
00AB01/11
43TG22/00
78RC09/34
......
......
and a second file , file 2 having two columns like
78RC09/34 1
45FD11/11 2
00AB01/11 3
43TG22/00 4
......
...... (8 Replies)
Hi all,
I have two files as below. I need to compare field 2 of file 1 against field 1 of file 2 and field 5 of file 1 against filed 2 of file 2. If both matches , then create a result file 1 with first file data and if not matches , then create file with first fie data. Please help me in... (12 Replies)
Discussion started by: sivarajb
12 Replies
LEARN ABOUT DEBIAN
probalign
PROBALIGN(1) User Commands PROBALIGN(1)NAME
probalign - Align sequences in MFAFILE(s) and print result to standard output
DESCRIPTION
PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the standard output. Written by Satish Chikkagoudar and
Usman Roshan using code from PROBCONS version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein).
PROBALIGN 1.4 comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions.
See the README file for details.
Usage:
probalign [OPTION]... [MFAFILE]...
Description:
Align sequences in MFAFILE(s) and print result to standard output
-clustalw
use CLUSTALW output format instead of MFA
-v, --verbose
report progress while aligning (default: off)
-a, --alignment-order
print sequences in alignment order rather than input order (default: off)
-T, -temperature
Sets the thermodynamic temperature parameter
(default: 5 (for protein data mode), 1 ( for nucleotide data mode)).
-score_matrix, --score_matrix
Sets the type of scoring matrix used to calculate the posterior probabilities (default: gonnet_160, representing gonnet 160, refer
README for details)
-go, --gap-open
This option can be used to specify the gap open parameter. The default for Gonnet 160 (protein) is 22 and nucleotide (simple matrix)
is 4.
-ge, --gap-extension
This option can be used to specify the gap extension parameter. The default for Gonnet 160 (protein) is 1 and nucleotide (simple
matrix) is 0.25.
-nuc
Specify this option to indicate that inputted sequences are nucleotide sequences
-prot
Specify this option to indicate that inputted sequences are protein sequences [DEFAULT]
-showPP
Outputs the posterior probabilities of alignment columns as a new sequence named Posterior Probabilities (The probability values are
scaled to be between integers between 0 and 9).
probalign 1.4 May 2011 PROBALIGN(1)