Duplicate_SeqIds Blast database

Question

[sukesh1411]

Hi

I could not create a blast database for nucleotide i.e nt text file which has sequences in fasta format.

because Error: Duplicate seq_ids are found.

How can remove this dup seq_ids. Can anyone help me on this

Answer 1

[Prasad]

you can go through the How To Remove The Same Sequences In The Fasta Files?

using cd-hit or uclust tools (with 100% identity and coverage cutoff) you can remove the duplicates.

[sukesh1411]

I am trying with uclust tools. The nt file which i downloaded from blast database is text file which has sequences in fasta format. This text format is not accepted by uclust tools. How can i convert text to fasta format.

[Prasad]

can you post few lines as an example from you text file

[sukesh1411]

gi|4|emb|X17276.1| Giant Panda satellite 1 DNA GATCCTCCCCAGGCCCCTACACCCAATGTGGAACCGGGGTCCCGAATGAAAATGCTGCTGTTCCCTGGAGGTGTTTTCCT GGACGCTCTGCTTTGTTACCAATGAGAAGGGCGCTGAATCCTCGAAAATCCTGACCCTTTTAATTCATGCTCCCTTACTC ACGAGAGATGATGATCGTTGATATTTCCCTGGACTGTGTGGGGTCTCAGAGACCACTATGGGGCACTCTCGTCAGGCTTC CGCGACCACGTTCCCTCATGTTTCCCTATTAACGAAGGGTGATGATAGTGCTAAGACGGTCCCTGTACGGTGTTGTTTCT GACAGACGTGTTTTGGGCCTTTTCGTTCCATTGCCGCCAGCAGTTTTGACAGGATTTCCCCAGGGAGCAAACTTTTCGAT GGAAACGGGTTTTGGCCGAATTGTCTTTCTCAGTGCTGTGTTCGTCGTGTTTCACTCACGGTACCAAAACACCTTGATTA TTGTTCCACCCTCCATAAGGCCGTCGTGACTTCAAGGGCTTTCCCCTCAAACTTTGTTTCTTGGTTCTACGGGCTG gi|7|emb|X51700.1| Bos taurus mRNA for bone Gla protein GTCCACGCAGCCGCTGACAGACACACCATGAGAACCCCCATGCTGCTCGCCCTGCTGGCCCTGGCCACACTCTGCCTCGC TGGCCGGGCAGATGCAAAGCCTGGTGATGCAGAGTCGGGCAAAGGCGCAGCCTTCGTGTCCAAGCAGGAGGGCAGCGAGG TGGTGAAGAGACTCAGGCGCTACCTGGACCACTGGCTGGGAGCCCCAGCCCCCTACCCAGATCCGCTGGAGCCCAAGAGG GAGGTGTGTGAGCTCAACCCTGACTGTGACGAGCTAGCTGACCACATCGGCTTCCAGGAAGCCTATCGGCGCTTCTACGG CCCAGTCTAGAGCTTGCAGCCCTGCCCACCTGGCTGGCAGCCCCCAGCTCTGGCTTCTCTCCAGGACCCCTCCCCTCCCC GTCATCCCCGCTGCTCTAGAATAAACTCCAGAAGAGG

[Prasad]

Just > is missing from the header line. If your file is small you can just replace gi| with >gi|. If the file is huge use any code

perl -ne '{if ($_=~/^gi/){print ">",$_;}else{print}}'  input_file >out_file

[Prasad]

the same question you have already posted here. It seems you have a fasta file. I assume you have got the answer for this question