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how can i get multiple fasta sequences using blast?

thank you for reading. i'm currently trying to making a database of NGS paired-end sequence data. i have 2 sequence data for each locus now(named R1 and R2.) i've already finshed getting sequence names whose sequences passed through the quality checks using grep command. however, i can not figure out how to get the
sequences by using just one file as a query which contains the sequence names at the same time. i'd appriciate it if you could tell me that kind of command. thank you.

gene
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written by s816320018 • s816320018

Not exactly sure what you are asking but you can use filterbyname.sh from BBMap suite to extract reads you need from a larger fastq file. Run the program on its own to look at in-line help on other options. The program should also work with fasta sequences.

You should not need to use blast+.

$ filterbyname.sh

Written by Brian Bushnell
Last modified September 1, 2016

Description:  Filters reads by name.

Usage:  filterbyname.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> names=<string,string,string> include=<t/f>

names=          A list of strings or files.  The files can have one name per line, or
                be a standard read file (fasta, fastq, or sam).
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written by GenoMax GenoMax

thank you for your prompt reply. i'm sorry for my unclear contexts. i have some marker sequences now and i want to extract sequences which contains the markers from both R1 and 2 sequences. anyway, i'll try that command. thank you.

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written by s816320018 • s816320018

This link might help:

https://ncbi.github.io/magicblast/cook/paired.html

For SRA accessions Magic-BLAST determines whether reads are paired and maps them appropriately.

For reads in FASTA and FASTQ files paired reads can either be in a single file, or two files.

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written by Fatima Fatima

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