How to extract sequence from fasta by sequence similarity

Question

[Janey]

Hello I have two fasta files with different IDs which belongs to the two genotypes . first fasta file Consists of 100 contigs while second file include 100,000 contigs. I want to extranct the same contigs of first file from second file. I thank you for your suggestions.

Thank you

[Farbod]

Hi,

You can convert your 100,000 contig fasta to tsv using fasta_formatter from the FASTX-Toolkit

Then use grep with the --file option to supply your text file (list of 100 IDs) of patterns.

You cane use Galaxy, too.

Answer 1

[venu]

Assuming you have sequence as one string (Otherwise linearize both fasta files)

sed '/^>/d' file_1.fa | while read -r line; do grep -B 1 "$line" file_2.fa >> foo.res.txt; done

With this approach you don't need to worry if the headers are different for same contig in 2 files. If the header is same in two files, you can proceed with faSomeRecords as mentioned in other answers.

Answer 2

[Sej Modha]

You can either BLAST them against each other or use a clustering program like cdhit to cluster identical sequences together.

Answer 3

[Farbod]

Dear Janey, Hi

You can create a list fo your 100 IDs (a text file, each ID in a new line, it is your listFile) and then use some script/tools same as faSomeRecords to extract the sequences of those IDs from the 100,000 contig file (which is now in.fa):

./faSomeRecords in.fa listFile out.fa

Hope I get your point correctly

~ Best

Answer 4

[Janey]

thanks for answers of my friends but i need tool or software that finally tell me: ID: 23 from file 1 has similar seuence to ID; 666 from file 2

[Farbod]

I think your title was not very clear ;-)

And the threshold of "similarity" is a problem here.

Are you searching for exact matches ?

[Janey]

hi farbod yes about 98-100% similarity

[GenoMax]

Then just search the second file (think of it as "reference") using the first using any NGS aligner (and look for 100% matches?). bowtie v.1 may be the best tool if these are raw Illumina sequences.

Answer 5

[nuketbilgen]

Hi, How about zipped fastq files? zgrep command is not working. :/