Analysis of base composition of a sequence

[genefinder]

Dear member,

I have a simple question.

Could anyone suggest me a software (free ware) which gives me base composition of a sequence i.e (%A, %T, %G and %C)? My gene sequences are 8.5 kb and less.

Thanks for the help!

[Heisman]

If you google you may find this link: http://unix.stackexchange.com/questi...r-in-each-line

Here's a bash script that will work. Run it as ./script input_sequence:

#! /bin/bash
input=$1
A_total=`sed 's/[^A]//g' $input | awk '{ print length }'`
C_total=`sed 's/[^C]//g' $input | awk '{ print length }'`
G_total=`sed 's/[^G]//g' $input | awk '{ print length }'`
T_total=`sed 's/[^T]//g' $input | awk '{ print length }'`
Total=$(( $A_total + $C_total + $G_total + $T_total ))
A_percent=`echo "scale=3; $A_total / $Total" | bc`
C_percent=`echo "scale=3; $C_total / $Total" | bc`
G_percent=`echo "scale=3; $G_total / $Total" | bc`
T_percent=`echo "scale=3; $T_total / $Total" | bc`
echo A% = "$A_percent"
echo C% = "$C_percent"
echo G% = "$G_percent"
echo T% = "$T_percent"

[genefinder]

Hi Heisman,

Thank you for the reply.

Isn't there any freeware where we can just input the sequence in fasta or any other format and it gives a summary of A, T, G and Cs?

I am really weak in script writing.

[dariober]

Isn't there any freeware where we can just input the sequence in fasta or any other format and it gives a summary of A, T, G and Cs?

I think bedtools nuc in the bedtools suite might do what you want:

bedtools nuc -fi myfasta.fa -bed mybed.bed

The output will have counts of A,C,T,G and other stats for each interval in the bed file. Put in the bed file the start position (0) and end position of your fasta sequence/genome to summarize the entire sequence.

Good luck
Dario

[rhinoceros]

Hi Heisman,

Thank you for the reply.

Isn't there any freeware where we can just input the sequence in fasta or any other format and it gives a summary of A, T, G and Cs?

I am really weak in script writing.

That's exactly what Heisman gave you. If you want something with a GUI, you could open your sequence in for example Artemis and check the stats there..

[westerman]

Try one of the EMBOSS servers (http://emboss.sourceforge.net/servers/#portals) or the public Galaxy. Those should be GUI-based. Heck we even have one here at Purdue although it is hosted from one of our smaller computers and won't be suitable for large projects.