## Python: find the minimum in all rows

Python: find the minimum in all rows
# 1
05-16-2013
Python: find the minimum in all rows

I am using Biopython to process an alignment in fasta format. I need to slice the sequences where there is the first stop codon. So I divided my alignment in codons and found the stop.
I then found the first codon position using enumerate().
But I found the minimum for each row. However I need to find the minimum (storing it where it won't be reset when it does the next row), determine which of those is smallest. So that I can slice all the sequences in the same place.

pstop gives me the min for each row and I want to get the min of those min
to slice everything according to that min.
Thanks you very much for your help!
 Homa View Public Profile for Homa Find all posts by Homa

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```KALIGN(1)							Kalign User Manual							 KALIGN(1)

NAME
kalign - performs multiple alignment of biological sequences.

SYNOPSIS
kalign [infile.fasta] [outfile.fasta] [Options]

kalign [-i infile.fasta] [-o outfile.fasta] [Options]

kalign [< infile.fasta] [> outfile.fasta] [Options]

DESCRIPTION
Kalign is a command line tool to perform multiple alignment of biological sequences. It employs the Muth?Manber string-matching algorithm,
to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an
approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global
alignment.

OPTIONS
-s -gpo -gapopen -gap_open x
Gap open penalty .

-e -gpe -gap_ext -gapextension x
Gap extension penalty.

-t -tgpe -terminal_gap_extension_penalty x
Terminal gap penalties.

-m -bonus -matrix_bonus x
A constant added to the substitution matrix.

-c -sort <input, tree, gaps.>
The order in which the sequences appear in the output alignment.

-g -feature
Selects feature mode and specifies which features are to be used: e.g. all, maxplp, STRUCT, PFAM-A?

-same_feature_score
Score for aligning same features.

-diff_feature_score
Penalty for aligning different features.

-d -distance <wu, pair>
Distance method

-b -tree -guide-tree <nj, upgma>
Guide tree method.

-z -zcutoff
Parameter used in the wu-manber based distance calculation.

-i -in -input
Name of the input file.

-o -out -output
Name of the output file.

-a -gap_inc
Increases gap penalties depending on the number of existing gaps.

-f -format <fasta, msf, aln, clu, macsim>
The output format.

-q -quiet
Print nothing to STDERR. Read nothing from STDIN.

REFERENCES
o   Timo Lassmann and Erik L.L. Sonnhammer (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics
6:298

o   Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer (2009) Kalign2: high-performance multiple alignment of protein and nucleotide
sequences allowing external features. Nucleic Acid Research 3:858?865.

AUTHORS
Timo Lassmann <timolassmann@gmail.com>
Upstream author of Kalign.

Charles Plessy <plessy@debian.org>
Wrote the manpage.