I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format.
Each individual FASTA file looks something like this:
(example for SRR5678544 file)
>SRR5678544.1 HWI-ST1146_88:5:1112:6472:81473 length=194 CCATGCGGGGTATCGTATGCTTCCTTCTGCACTACCCTTTAGCTGTTCTATATGCTGCCACTCCTCAATTGGATTAGTCTCATCCTTCAATGCTATCACAAGAAGTAGAGACACAAATGCAAGAGGAGCATATAAATTACAAAACACCATCACTGAGGGCCCTAAAGCGGTTCCCACGAAAAAAAGGAGAGTAG >SRR5678544.2 HWI-ST1146_88:5:1113:13218:62635 length=194 TGGATGGTGGTTGGGAGTGGTAAGGTTGAATGAGACACGGTAACGAGTGGGGAGGTAGGGTAATGGAGGGTAAGTTGAGAGACAGGTTCGTCAGGGGACACACCACACCACACCCACACCCACACACCCACACACCACACCCACACACCACACCCACACCCACACCCCCACACACCACACCCCCACCCCACCCA >SRR5678544.3 HWI-ST1146_88:5:2206:11224:22269 length=194 GTCTCTTAACTTACCCTCCATTACCCTACCTCCCGACTCGTTACCCTGTCTCATTCAACCATACCACTCCCGACCACCATCCATCCCTCTACTTACTACAGTATGGTGAGTGGGACATGGTGGATGGTAGGGTAAGTGGCAGTGGAGTTGGATATGGGCAATTGGAGGGTAACGGTTATGGTGGACGGGGGGTG
And so on and so forth. (Ignore the " and ' marks I had to input those to format it right on here)
Question 1: Can someone explain why this file has so many sequences (>)? Every FASTA file I have worked with has one line with ">" at the top and a header sentence followed by a single big paragraph of the genome sequence.
Question 2: If I wanted to combine all the sequences in a single FASTA file to look like a "normal" FASTA file - just a single paragraph - how would I do that?
Reasoning: I'm asking simply because I need to make a BLAST database out of the 157 sequences and the "makeblastdb" command only takes in a single file as the input. I was going to try and combine each individual FASTA file into single paragraphs and then make a huge FASTA file that includes all 157 sequences separated by ">".