to find same or similar sequences within fasta seq

Question

[Kurban]

Hello, I am trying to find out the best way to find same or similar sequences to the defined sequence within the transcriptome sequences in fasta file, which is assembled from RNA-seq data. I know there are many tools, but I don't know which one is developed for this purpose. could any one give me some tips? thanks?

[Josh Herr]

I'm not clear on what exactly you are looking to do -- compare sequences from different samples or within the same sample? There are many different strategies to do both - from clustering (usearch/UPARSE/cd-HIT, etc) to alignment (BLAST, etc.). Can you please clarify your original post with your research question?

[Kurban]

sorry @Josh Herr, I have not been clear.

I have a fasta file which contain around 144,000 transcripts/sequences(transcriptome of an insect). My boss gave me several nucleotide sequences and asked me is there any similar or same sequences in the fasta file with those sequences? If any, which ones and how are their similarity?

I want to align those sequences one by one with the transcriptome(fasta file).

I am new at this kind of analysis

[Devon Ryan]

Sounds like blast would be a good solution. You can install it locally and use it from the command line.

[Kurban]

Thank you @Josh Herr ,@Siva and @Geek_y.

Answer 1

[Siva]

You can create a BLAST database of those 144,000 transcripts and do BLASTN search using the nucleotide sequences as query.

Answer 2

[GouthamAtla]

You can use cd-hit-est or usearch for this purpose. They will make one representative sequence from similar sequences, which is based on user defined % similarity.

If you need to compare them against another set of sequences, you need to perform blast or any similar alignment.

[GouthamAtla]

Free version of usearch (32 bit) will be very slow.