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Sara
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I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my sequence, at first iteration I got 1000 hits and among them there were a lot of redundant sequences!

My sequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. All of these IDs were from RefSeq! In other iterations and after adjusting format options, I got this redundancy with other sequences from other species. My sequence is related to a chain of a multichain protein (E.coli fumarate reductase)

For example, when using NP_418578 as a query, I found WP_078165098.1, WP_064226696.1, WP_062863447.1, WP_001401474.1 and other that were identical.

I want to know what is wrong with Refseq. Is it really a Reference sequence database? If it is, where does this redundancy come from and why?

I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my sequence, at first iteration I got 1000 hits and among them there were a lot of redundant sequences!

My sequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. All of these IDs were from RefSeq! In other iterations and after adjusting format options, I got this redundancy with other sequences from other species.

For example, when using NP_418578 as a query, I found WP_078165098.1, WP_064226696.1, WP_062863447.1, WP_001401474.1 and other that were identical.

I want to know what is wrong with Refseq. Is it really a Reference sequence database? If it is, where does this redundancy come from and why?

I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my sequence, at first iteration I got 1000 hits and among them there were a lot of redundant sequences!

My sequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. All of these IDs were from RefSeq! In other iterations and after adjusting format options, I got this redundancy with other sequences from other species. My sequence is related to a chain of a multichain protein (E.coli fumarate reductase)

For example, when using NP_418578 as a query, I found WP_078165098.1, WP_064226696.1, WP_062863447.1, WP_001401474.1 and other that were identical.

I want to know what is wrong with Refseq. Is it really a Reference sequence database? If it is, where does this redundancy come from and why?

Added information from the OP's comment and cleaned up the question.
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I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my sequence, at first iteration I got 1000 hits thatand among them there were a lot of redundant sequences! 

My seqencesequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. All of these IDs were all from RefseqRefSeq! In other iterations and after adjusting format options, I got this redundancy with other sequences from other species.

For example, when using NP_418578 as a query, I found WP_078165098.1, WP_064226696.1, WP_062863447.1, WP_001401474.1 and other that were identical.

I want to know what is wrong with Refseq?. Is it really a Reference sequence database? If it is, where comesdoes this redundancy come from and why?

I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my sequence, at first iteration I got 1000 hits that among them there were a lot of redundant sequences! My seqence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. All of these IDs were all from Refseq! In other iterations and after adjusting format options, I got this redundancy with other sequences from other species. I want to know what is wrong with Refseq? Is it really a Reference sequence database? If it is, where comes this redundancy and why?

I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my sequence, at first iteration I got 1000 hits and among them there were a lot of redundant sequences! 

My sequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. All of these IDs were from RefSeq! In other iterations and after adjusting format options, I got this redundancy with other sequences from other species.

For example, when using NP_418578 as a query, I found WP_078165098.1, WP_064226696.1, WP_062863447.1, WP_001401474.1 and other that were identical.

I want to know what is wrong with Refseq. Is it really a Reference sequence database? If it is, where does this redundancy come from and why?

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gringer
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Is there anything wrong with Refseq? Duplicate long hits from PSI-BLAST

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Sara
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