Each hit is for an alternate version of the human genome.
ref|NT_167247.1| Homo sapiens chromosome 6 genomic contig, GRCh37.p2 reference
assembly alternate locus group ALT_REF_LOCI_5 Length=4833398
ref|NT_113891.2| Homo sapiens chromosome 6 genomic contig, GRCh37.p2 reference
assembly alternate locus group ALT_REF_LOCI_2 Length=4795371
-
Different starting position in Genbank blast result?
I am new to this field and this probably a very ignorant question.
However, when I did a blast search with following sequence, "TGTCTTTGGACATGTAAGAATTGGAGGAAAATAAATGTGGATTTGGGAAACTTTGAGG" blast returned me this following result. As seen in the result, matched sequences are in same chromosome yet seemed to have different indices. Thus thinking those are repeated regions, I was trying to locate those. However, I could find only one not even two. My assumption is that those numbers are not really indices. Can anyone help me to understand this problem? Thank you.
>ref|NT_167247.1| Homo sapiens chromosome 6 genomic contig, GRCh37.p2 reference
assembly alternate locus group ALT_REF_LOCI_5
Length=4833398
Features in this part of subject sequence:
large proline-rich protein BAT2
Score = 108 bits (58), Expect = 7e-22
Identities = 58/58 (100%), Gaps = 0/58 (0%)
Strand=Plus/Plus
Query 1 TGTCTTTGGACATGTAAGAATTGGAGGAAAATAAATGTGGATTTGGGAAACTTTGAGG 58
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 2970579 TGTCTTTGGACATGTAAGAATTGGAGGAAAATAAATGTGGATTTGGGAAACTTTGAGG 2970636
>ref|NT_167245.1| Homo sapiens chromosome 6 genomic contig, GRCh37.p2 reference
assembly alternate locus group ALT_REF_LOCI_3
Length=4610396
Features in this part of subject sequence:
large proline-rich protein BAT2
Score = 108 bits (58), Expect = 7e-22
Identities = 58/58 (100%), Gaps = 0/58 (0%)
Strand=Plus/Plus
Query 1 TGTCTTTGGACATGTAAGAATTGGAGGAAAATAAATGTGGATTTGGGAAACTTTGAGG 58
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 2876461 TGTCTTTGGACATGTAAGAATTGGAGGAAAATAAATGTGGATTTGGGAAACTTTGAGG 2876518
>ref|NT_113891.2| Homo sapiens chromosome 6 genomic contig, GRCh37.p2 reference
assembly alternate locus group ALT_REF_LOCI_2
Length=4795371
Features in this part of subject sequence:
large proline-rich protein BAT2
Score = 102 bits (55), Expect = 3e-20
Identities = 57/58 (99%), Gaps = 0/58 (0%)
Strand=Plus/Plus
Query 1 TGTCTTTGGACATGTAAGAATTGGAGGAAAATAAATGTGGATTTGGGAAACTTTGAGG 58
|||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct 3100500 TGTCTTTGGACACGTAAGAATTGGAGGAAAATAAATGTGGATTTGGGAAACTTTGAGG 3100557
-
At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...09-26-2023, 06:26 AM -
Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...09-07-2023, 11:15 PM -
Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.
Whole Transcriptome RNA-seq
Whole transcriptome sequencing...08-31-2023, 11:07 AM
Leave a comment: